Showing papers in "Soil Biology & Biochemistry in 2019"

Rhizosphere size and shape: Temporal dynamics and spatial stationarity

Abstract: The soil volume affected by roots – the rhizosphere – is one of the most important microbial hotspots determining the processes, dynamics and cycling of carbon (C), nutrients and water in terrestrial ecosystems. Rhizosphere visualization is necessary to understand, localize and quantify the ongoing processes and functions, but quantitative conclusions are very uncertain because of: 1) the continuum of the parameters between the root surface and root-free soil, i.e., there are no sharp borders, 2) differences in the distributions of various parameters (C, nutrients, pH, enzyme and microbial activities, gases, water etc.) across and along roots, 3) temporal changes of the parameters and processes with root growth as well as with water and C flows. In situ techniques: planar optodes, zymography, sensitive gels, 14C and neutron imaging as well as destructive approaches (thin layer slicing) have been used to analyze the rhizosphere extent and the gradients of various physico-chemical and biological characteristics: pH, CO2, O2, redox potential, enzyme activities, content of water, nutrients and excess elements, and organic compounds. A literature analysis allows the conclusion that: i) the rhizosphere extent for most of the parameters assessed by non-destructive visualization techniques is 0.5–4 mm but exceeds 4 mm for gases, nitrate, water and redox potential. ii) The rhizosphere extent of nutrients (N, P) is decoupled from the extent of the corresponding enzyme activities. iii) The imbalance between element flows to and uptake by roots may lead to accumulation of excess elements and formation of root carapaces (e.g. CaCO3 rhizoliths, Fe plaque) ranging up to a few cm. iv) All destructive approaches show a much (3–5 times) larger rhizosphere extent compared to visualization techniques. These conclusions are crucial for a mechanistic understanding of rhizosphere properties and functioning, estimation of the nutrient stocks available to roots, and for rhizosphere modelling considering root growth and architecture. Overall, roots function as ecosystem engineers and build their environment, serving as the main factors shaping rhizosphere extent. Sharp gradients are formed within a few days for nutrients and enzymes, but more time is necessary for the establishment of specific microbial communities. Despite the very strong dynamics of most parameters, their stationarity is reached within a few days because the release of C and enzymes or nutrient uptake are very quickly compensated by utilization by surrounding microorganisms or/and sorption and diffusion processes. We conclude that despite the dynamic nature of each property, the rhizosphere gradients, their extent and shape are quasi-stationary because of the opposite directions of their formation processes.

Long-term manure application increases soil organic matter and aggregation, and alters microbial community structure and keystone taxa

Abstract: Microbes play pivotal roles in soil organic matter (SOM) turnover: formation and decomposition. Organic fertilizers play crucial role for SOM accumulation, aggregate formation and influence microbial community composition and co-occurrence networks in microhabitats. Here, we investigated prokaryotic and fungal communities and their co-occurrence networks in four aggregate size classes in upland Ultisol following 27 years of mineral and/or organic fertilizer (rice straw, peanut straw, radish, or pig manure) application. Organic fertilizers and aggregate size classes have main and interactive effects on SOM content in aggregates (p 250 μm) than microaggregates (

The ratio of Gram-positive to Gram-negative bacterial PLFA markers as an indicator of carbon availability in organic soils

Abstract: Despite recent progress in understanding soil microbial responses to carbon (C) limitation, the functional shifts in microbial community structure associated with decreasing soil C availability and changes in organic matter chemistry remain poorly known. It has been proposed that Gram-negative (GN) bacteria use more plant-derived C sources that are relatively labile, while Gram-positive (GP) bacteria use C sources derived from soil organic matter that are more recalcitrant. Because these two groups may differ in how they influence the fate of different C forms in soils, it is important to understand how they vary across ecosystems that differ in their vegetation cover and ecosystem productivity or across environmental gradients. In this study, we used a 19-year plant functional group removal experiment across a long term post-fire chronosequence to assess how microbial community structure (assessed using phospholipids fatty acids; PLFAs) and the association of bacterial functional groups (specifically, the GP:GN ratio) responded to changes in organic matter chemistry (measured via nuclear magnetic resonance; NMR). We found that the GP:GN ratio increased upon removal of shrubs and tree roots and with decreasing ecosystem productivity along the chronosequence, thus showing the greater dependence of GN than GP bacteria on more labile plant-derived C. Overall, GN bacteria were associated with simple C compounds (alkyls) whereas GP bacteria were more strongly associated with more complex C forms (carbonyls). Therefore, we conclude that the GP:GN ratio has potential as a useful indicator of the relative C availability for soil bacterial communities in organic soils, and can be used as a coarse indicator of energy limitation in natural ecosystems.

Soil multifunctionality is affected by the soil environment and by microbial community composition and diversity.

Abstract: Microorganisms are critical in mediating carbon (C) and nitrogen (N) cycling processes in soils. Yet, it has long been debated whether the processes underlying biogeochemical cycles are affected by the composition and diversity of the soil microbial community or not. The composition and diversity of soil microbial communities can be influenced by various environmental factors, which in turn are known to impact biogeochemical processes. The objectives of this study were to test effects of multiple edaphic drivers individually and represented as the multivariate soil environment interacting with microbial community composition and diversity, and concomitantly on multiple soil functions (i.e. soil enzyme activities, soil C and N processes). We employed high-throughput sequencing (Illumina MiSeq) to analyze bacterial/archaeal and fungal community composition by targeting the 16S rRNA gene and the ITS1 region of soils collected from three land uses (cropland, grassland and forest) deriving from two bedrock forms (silicate and limestone). Based on this data set we explored single and combined effects of edaphic variables on soil microbial community structure and diversity, as well as on soil enzyme activities and several soil C and N processes. We found that both bacterial/archaeal and fungal communities were shaped by the same edaphic factors, with most single edaphic variables and the combined soil environment representation exerting stronger effects on bacterial/archaeal communities than on fungal communities, as demonstrated by (partial) Mantel tests. We also found similar edaphic controls on the bacterial/archaeal/fungal richness and diversity. Soil C processes were only directly affected by the soil environment but not affected by microbial community composition. In contrast, soil N processes were significantly related to bacterial/archaeal community composition and bacterial/archaeal/fungal richness/diversity but not directly affected by the soil environment. This indicates direct control of the soil environment on soil C processes and indirect control of the soil environment on soil N processes by structuring the microbial communities. The study further highlights the importance of edaphic drivers and microbial communities (i.e. composition and diversity) on important soil C and N processes.

Microbial growth and carbon use efficiency in soil: Links to fungal-bacterial dominance, SOC-quality and stoichiometry

Abstract: Microbial decomposers are responsible for the breakdown of organic matter (OM) and thus regulate soil carbon (C) stocks. During the decomposition of OM, microorganisms can use the assimilated C for biomass production or respire it as CO2, and the fraction of growth to total assimilation defines the microbial carbon-use efficiency (CUE). As such, CUE has direct consequences for how microbial decomposers affect the balance of C between atmosphere and soil. We estimated fungal and bacterial growth in C units in microcosm systems with submerged plant litter. We established conversion factors between bacterial and fungal growth to biomass and applied this to a dataset representing 9 different sites in temperate forest soils, temperate agricultural soils, and subarctic forest soils, to estimate growth rates of fungi and bacteria in units of C, to estimate the dominance of the two decomposer groups, and to compare these values to respiration to estimate the microbial CUE. We observed that fungal-to-bacterial growth ratios (F:B) ranged from 0.02 to 0.44, and that the fungal dominance was higher in soils with lower C:N ratio and higher C-quality. We found a negative exponential relationship between the dominance of fungi and the microbial CUE. CUE ranged from 0.03 to 0.30, and values clustered most strongly according to site rather than level of soil N. CUE was higher in soil with high C:N ratio and high C-quality. However, within each land-use type, a high mineral N-content did result in lower F:B and higher resulting CUE. In conclusion, a higher soil C-quality coincided with lower F:B and higher CUE across the surveyed sites, while a higher N availability did not. A higher N availability resulted in higher CUE and lower F:B within each site suggesting that site-specific differences such as the effect of plant community via e.g. plant litter and rhizosphere input, overrode the influence of N-availability.

Rare taxa of alkaline phosphomonoesterase-harboring microorganisms mediate soil phosphorus mineralization

Abstract: As a homologous gene encoding microbial alkaline phosphomonoesterase, the expression of phoD is critically controlled by P availability and thus contributes to the mineralization of soil organic P under P-depleted condition. However, its role in the regulation of soil P turnover is largely unknown due to the complex coupling of physiochemical and biological processes in the P cycle, especially in paddy field. We hypothesized that 1) P fertilization would decrease the abundance of phoD gene and change the composition of phoD-harboring microbial community and 2) the high abundance of phoD-harboring microorganisms in P-poor soil would stimulate the synthesis of alkaline phosphomonoesterase, thus mitigating P limitation via the mineralization of organic P. After 42 days of rice growth, the phoD abundance negatively correlated with soil P availability, and it was significantly higher in non-fertilized treatments than in P-fertilized treatments for both rhizosphere and bulk soils. A stronger competition among phoD-harboring microorganisms was detected in non-fertilized soil than in P-fertilized soil, with Bradyrhizobium, Methylobacterium, and Methylomonas being the dominant taxa in all samples. However, the high phoD gene abundance under P-poor condition was mainly due to the growth of rare operational taxonomic units (OTUs) affiliated to Actinobacteria and Cyanobacteria (relative abundance

Cover cropping and no-till increase diversity and symbiotroph:saprotroph ratios of soil fungal communities

Abstract: Fungi are important members of soil microbial communities in row-crop and grassland soils, provide essential ecosystem services such as nutrient cycling, organic matter decomposition, and soil structure, but fungi are also more sensitive to physical disturbance than other microorganisms. Adoption of conservation management practices such as no-till and cover cropping shape the structure and function of soil fungal communities. No-till eliminates or greatly reduces the physical disturbance that re-distributes organisms and nutrients in the soil profile and disrupts fungal hyphal networks, while cover crops provide additional types and greater abundance of organic carbon sources. In a long-term, row crop field experiment in California's Central Valley we hypothesized that a more diverse and plant symbiont-enriched fungal soil community would develop in soil managed with reduced tillage practices and/or cover crops compared to standard tillage and no cover crops. We measured the interacting effects of tillage and cover cropping on fungal communities based on fungal ITS sequence assigned to ecological guilds. Functional groups within fungal communities were most sensitive to long-term tillage practices, with 45% of guild-assigned taxa responding to tillage, and a higher proportion of symbiotroph taxa under no-till. In contrast, diversity measures reflected greater sensitivity to cover crops, with higher phylogenetic diversity observed in soils managed with cover crops, though only 10% of guild-assigned taxa responded to cover crops. The relative abundance of pathotrophs did not vary across the management treatments. Cover cropping increased species diversity, while no-till shifted the symbiotroph:saprotroph ratio to favor symbiotrophs. These management-induced shifts in fungal community composition could lead to greater ecosystem resilience and provide greater access of crops to limiting resources.

Clarifying the interpretation of carbon use efficiency in soil through methods comparison

Abstract: Accurate estimates of microbial carbon use efficiency (CUE) are required to predict how global change will impact microbially-mediated ecosystem functions such as organic matter decomposition. Multiple approaches are currently used to quantify CUE but the extent to which estimates reflect methodological variability is unknown. This limits our ability to apply or cross-compare published CUE values. Here we evaluated the performance of five methods in a single soil under standard conditions. The microbial response to three substrate amendment rates (0.0, 0.05, and 2.0 mg glucose-C g−1 soil) was examined using: 13C and 18O isotope tracing approaches which estimate CUE based on substrate uptake and growth dynamics; calorespirometry which infers growth and CUE from metabolic heat and respiration rates; metabolic flux analysis where CUE is determined as the balance between biosynthesis and respiration using position-specific 13CO2 production of labeled glucose; and stoichiometric modeling which derives CUE from elemental ratios of microbial biomass, substrate, and exoenzyme activity. The CUE estimates we obtained differed by method and substrate concentration, ranging under in situ conditions from 0.6 for the substrate-specific methods that trace glucose use (13C method, calorespirometry, metabolic flux analysis). We explore the different aspects of microbial metabolism that each method captures and how this affects the interpretation of CUE estimates. We recommend that users consider the strengths and weaknesses of each method when choosing the technique that will best address their research needs.

Soil bacterial and fungal response to wildfires in the Canadian boreal forest across a burn severity gradient

Abstract: Global fire regimes are changing, with increases in wildfire frequency and severity expected for many North American forests over the next 100 years. Fires can result in dramatic changes to carbon (C) stocks and can restructure plant and microbial communities, with long-lasting effects on ecosystem functions. We investigated wildfire effects on soil microbial communities (bacteria and fungi) in an extreme fire season in the northwestern Canadian boreal forest, using field surveys, remote sensing, and high-throughput amplicon sequencing in upland and wetland sites. We hypothesized that vegetation community and soil pH would be the most important determinants of microbial community composition, while the effect of fire might not be significant, and found that fire occurrence, along with vegetation community, moisture regime, pH, total carbon, and soil texture are all significant predictors of soil microbial community composition. Burned communities become increasingly dissimilar to unburned communities with increasingly severe burns, and the burn severity index (an index of the fractional area of consumed organic soils and exposed mineral soils) best predicted total bacterial community composition, while whether a site was burned or not was the best predictor for fungi. Globally abundant taxa were identified as significant positive fire responders in this system, including the bacteria Massilia sp. (64 × more abundant with fire) and Arthrobacter sp. (35 × ), and the fungi Penicillium sp. (22 × ) and Fusicladium sp. (12 × ). Bacterial and fungal co-occurrence network modules were characterized by fire responsiveness as well as pH and moisture regime. Building on the efforts of previous studies, our results consider a particularly wide range of soils, vegetation, and burn severities, and we identify specific fire-responsive microbial taxa and suggest that accounting for burn severity improves our understanding of microbial response to fires.

Review and synthesis of the effects of elevated atmospheric CO2 on soil processes: No changes in pools, but increased fluxes and accelerated cycles

Abstract: Atmospheric change encompassing a rising carbon dioxide (CO2) concentration is one component of Global Change that affects various ecosystem processes and functions. The effects of elevated CO2 (eCO2) on belowground processes are incompletely understood due to complex interactions among various ecosystem fluxes and components such as net primary productivity, carbon (C) inputs to soil, and the living and dead soil C and nutrient pools. Here we summarize the literature on the impacts of eCO2 on 1) cycling of C and nitrogen (N), 2) microbial growth and enzyme activities, 3) turnover of soil organic matter (SOM) and induced priming effects including N mobilization/immobilization processes, and 4) associated nutrient mobilization from organic sources, 5) water budget with consequences for soil moisture, 6) formation and leaching of pedogenic carbonates, as well as 7) mobilization of nutrients and nonessential elements through accelerated weathering. We show that all effects in soil are indirect: they are mediated by plants through increased net primary production and C inputs by roots that foster intensive competition between plants and microorganisms for nutrients. Higher belowground C input from plants under eCO2 is compensated by faster C turnover due to accelerated microbial growth, metabolism and respiration, higher enzymatic activities, and priming of soil C, N and P pools. We compare the effects of eCO2 on pool size and associated fluxes in: soil C stocks vs. belowground C input, microbial biomass vs. CO2 soil efflux vs. various microbial activities and functions, dissolved organic matter content vs. its production, nutrient stocks vs. fluxes etc. Based on these comparisons, we generalize that eCO2 will have little impacts on pool size but will strongly accelerate the fluxes in biologically active and stable pools and consequently will accelerates biogeochemical cycles of C, nutrients and nonessential elements.

Comammox Nitrospira play an active role in nitrification of agricultural soils amended with nitrogen fertilizers

Abstract: The recent discovery of complete ammonia oxidizers (comammox Nitrospira) challenged the paradigm of the two-step nitrification mediated by two distinct groups of nitrifiers, and raised fundamental questions regarding their niche specialization and relative contribution to nitrification in agricultural soils. Previous studies suggest that comammox Nitrospira have an oligotrophic lifestyle and would outcompete canonical ammonia oxidizers (ammonia-oxidizing bacteria and ammonia-oxidizing archaea) under ammonia-limited conditions. Here, we demonstrated that comammox Nitrospira clade A were significantly more abundant than canonical ammonia oxidizers and 13CO2-DNA-stable isotope probing revealed that comammox Nitrospira clade A incorporated 13CO2 into their genomes in fertilized agricultural soils during the microcosm incubation. Phylogenetic analysis of the amoA gene revealed that 13CO2-labelled comammox Nitrospira clade A belonged to the Nitrospira inopinata-related cluster and a new cluster that was distinct from the known comammox isolates. These results demonstrated the potential important role of comammox Nitrospira in autotrophic ammonia oxidation in agricultural soils amended with nitrogen fertilizers and their lifestyle may be not strictly restricted to oligotrophic habitats. There is a potential contribution of comammox Nitrospira to soil nitrification, which calls re-evaluation of the microbial nitrogen cycling processes and the subsequent impacts on agriculture and the environment.

Effects of past and current drought on the composition and diversity of soil microbial communities

Abstract: Drought is well known to have strong effects on the composition and activity of soil microbial communities, and may be determined by drought history and drought duration, but the characterisation and prediction of these effects remains challenging. This is because soil microbial communities that have previously been exposed to drought may change less in response to subsequent drought events, due to the selection of drought-resistant taxa. We set up a 10-level drought experiment to test the effect of water stress on the composition and diversity of soil bacterial and fungal communities. We also investigated the effect of a previous long-term drought on communities in soils with different historical precipitation regimes. Saplings of the holm oak, Quercus ilex L., were included to assess the impact of plant presence on the effects of the drought treatment. The composition and diversity of the soil microbial communities were analysed using DNA amplicon sequencing of bacterial and fungal markers and the measurement of phospholipid fatty acids. The experimental drought affected the bacterial community much more than the fungal community, decreasing alpha diversity and proportion of total biomass, whereas fungal diversity tended to increase. The experimental drought altered the relative abundances of specific taxa of both bacteria and fungi, and in many cases these effects were modified by the presence of the plant and soil origin. Soils with a history of drought had higher overall bacterial alpha diversity at the end of the experimental drought, presumably because of adaptation of the bacterial community to drought conditions. However, some bacterial taxa (e.g. Chloroflexi) and fungal functional groups (plant pathogens and saprotrophic yeasts) decreased in abundance more in the pre-droughted soils. Our results suggest that soil communities will not necessarily be able to maintain the same functions during more extreme or more frequent future droughts, when functions are influenced by community composition. Drought is likely to continue to affect community composition, even in soils that are acclimated to it, tending to increase the proportion of fungi and reduce the proportion and diversity of bacteria.

Growth explains microbial carbon use efficiency across soils differing in land use and geology.

Abstract: The ratio of carbon (C) that is invested into microbial growth to organic C taken up is known as microbial carbon use efficiency (CUE), which is influenced by environmental factors such as soil temperature and soil moisture. How microbes will physiologically react to short-term environmental changes is not well understood, primarily due to methodological restrictions. Here we report on two independent laboratory experiments to explore short-term temperature and soil moisture effects on soil microbial physiology (i.e. respiration, growth, CUE, and microbial biomass turnover): (i) a temperature experiment with 1-day pre-incubation at 5, 15 and 25 °C at 60% water holding capacity (WHC), and (ii) a soil moisture/oxygen (O2) experiment with 7-day pre-incubation at 20 °C at 30%, 60% WHC (both at 21% O2) and 90% WHC at 1% O2. Experiments were conducted with soils from arable, pasture and forest sites derived from both silicate and limestone bedrocks. We found that microbial CUE responded heterogeneously though overall positively to short-term temperature changes, and decreased significantly under high moisture level (90% WHC)/suboxic conditions due to strong decreases in microbial growth. Microbial biomass turnover time decreased dramatically with increasing temperature, and increased significantly at high moisture level (90% WHC)/suboxic conditions. Our findings reveal that the responses of microbial CUE and microbial biomass turnover to short-term temperature and moisture/O2 changes depended mainly on microbial growth responses and less on respiration responses to the environmental cues, which were consistent across soils differing in land use and geology.

Comammox Nitrospira clade B contributes to nitrification in soil

Abstract: Comammox, one nitrifying microorganism carries out the complete oxidation of ammonia to nitrate, have been recently discovered, and are found in a wide range of environments, including soil. However, conditions under which they actually contribute to nitrification in soil have not yet been demonstrated. By 13CO2-based DNA stable isotope probing with real-time quantitative PCR and gene sequence, we reported two uncultured strains, which are closely related to comammox Nitrospira clade B, autotrophically grew in both forest and paddy soils only in the absence of ammonium amendment. Furthermore, all clade B amoA sequences amplified from isotopically enriched genomic DNA in both soils were derived from one or two phylotypes, indicating a low diversity of active comammox strains in soils.

Tree species identity surpasses richness in affecting soil microbial richness and community composition in subtropical forests

Abstract: Plant interactions and feedbacks with soil microorganisms play an important role in sustaining the functions and stability of terrestrial ecosystems, yet the effects of tree species diversity on soil microbial community in forest ecosystems are still not well understood. Here, we examined the effects of tree species richness (1–12 species) and the presence of certain influential tree species (sampling effect) on soil bacterial and fungal communities in Chinese subtropical forests, using high-throughput Illumina sequencing for microbial identification. We observed that beta rather than alpha diversities of tree species and soil microorganisms were strong coupled. Multivariate regression and redundancy analyses revealed that the effects of tree species identity dominated over tree species richness on the diversity and composition of bacterial and fungal communities in both organic and top mineral soil horizons. Soil pH, nutrients and topography were always identified as significant predictors in the best multivariate models. Tree species have stronger effect on fungi than bacteria in organic soil, and on ectomycorrhizal fungi than saprotrophic fungi in mineral topsoil. Concluding, tree species identity, along with abiotic soil and topographical conditions, were more important factors determining the soil microbial communities in subtropical forests than tree diversity per se.

pH and exchangeable aluminum are major regulators of microbial energy flow and carbon use efficiency in soil microbial communities

Abstract: The microbial partitioning of organic carbon (C) into either anabolic (i.e. growth) or catabolic (i.e. respiration) metabolic pathways represents a key process regulating the amount of added C that is retained in soil. The factors regulating C use efficiency (CUE) in agricultural soils, however, remain poorly understood. The aim of this study was to investigate substrate CUE from a wide range of soils (n = 970) and geographical area (200,000 km2) to determine which soil properties most influenced C retention within the microbial community. Using a 14C-labeling approach, we showed that the average CUE across all soils was 0.65 ± 0.003, but that the variation in CUE was relatively high within the sample population (CV 14.9%). Of the major properties measured in our soils, we found that pH and exchangeable aluminum (Al) were highly correlated with CUE. We identified a critical pH transition point at which CUE declined (pH 5.5). This coincided exactly with the point at which Al3+ started to become soluble. In contrast, other soil factors [e.g. total C and nitrogen (N), dissolved organic C (DOC), clay content, available calcium, phosphorus (P) and sulfur (S), total base cations] showed little or no relationship with CUE. We also found no evidence to suggest that nutrient stoichiometry (C:N, C:P and C:S ratios) influenced CUE in these soils. Based on current evidence, we postulate that the decline in microbial CUE at low pH and high Al reflects a greater channeling of C into energy intensive metabolic pathways involved in overcoming H+/Al3+ stress (e.g. cell repair and detoxification). The response may also be associated with shifts in microbial community structure, which are known to be tightly associated with soil pH. We conclude that maintaining agricultural soils above pH 5.5 maximizes microbial energy efficiency.

Fungal richness contributes to multifunctionality in boreal forest soil

Abstract: Boreal forests carry out functions that are critical to global biogeochemical cycling and climate regulation. Soil microbial diversity has been reported to drive multiple functions simultaneously (multifunctionality) in drylands and temperate ecosystems, however, the role and importance of bacterial and fungal diversity in driving multiple soil functions in boreal forest ecosystems remains poorly understood. We collected soils from 58 plots across upland and lowland (swamp) habitats in a boreal forest ecosystem to evaluate the linkages between fungal/bacterial diversity and multiple soil functions. Fungal and bacterial diversity were determined using 18S rDNA and 16S rDNA amplicons sequencing, and functions related to nutrient cycling (dissolved inorganic and organic nitrogen and carbon, nitrification) and climate regulation (CO2 and N2O emissions) were measured. The results showed that fungal but not bacterial richness was positively related to soil multifunctionality. We further used structural equation modelling to identify the effects of fungal and bacterial communities, and other environmental variables (moisture, pH, soil organic carbon and habitat types) on multifunctionality. Our model predicted 65.0% of the variation in soil multifunctionality, and confirmed that along with moisture and habitats, fungal richness and community composition were significantly and positively associated with multifunctionality. Finally, we identified specific fungal genera strongly associated with soil multifunctionality, and saprotrophic fungi were especially important for maintaining multiple soil functions. Our results suggest that potential losses in fungal diversity could result in reductions in soil functions particularly linked to nutrient cycling and climate regulation in boreal forests.

Can enzymatic stoichiometry be used to determine growth-limiting nutrients for microorganisms? - A critical assessment in two subtropical soils

Abstract: The measurement of potential enzymatic activities has been proposed as an efficient method to infer nutrient limitations for microorganisms in environmental samples. To validate this use, confirmation with direct methods of microbial growth responses to resource additions are required. We experimentally manipulated nutrient-poor soils from the afromontane subtropics with relatively low (grassland soils, ca. 4% soil carbon (C)) or high organic matter content (forest soils, ca. 13% soil C) with nutrient additions (plant material added at 8 mg C g−1 soil combined with mineral N and/or P to reach C:N:P mass-ratios of 10:1:1) in a multifactorial design for one month in order to shift the microbial community towards C-, N- or P-limitation. We then measured the responses of the most commonly measured indicator enzymes used to infer growth limiting nutrients, using s-1,4-glucosidase, s-1,4-N-acetylglucosaminidase and leucine aminopeptidase, and acid phosphatase as indicators for C-, N- and P-acquiring enzymatic activities, respectively. In the same soil samples, we also determined the responses in bacterial (3H-leucine incorporation) and fungal growth rates (14C-acetate incorporation into ergosterol) to nutrient supplements, and also verified these with biomass responses (microbial PLFA and ergosterol concentrations) to the factorial nutrient loading amendments. Ratios of C-, N-, and P-acquiring enzymes indicated that the grassland soils were primarily P-limited, and secondarily co-limited by C and N, while the forest soils were co-limited by C and P. However, short-term responses in growth rates and respiration to nutrient additions, along with long-term growth rate, respiration and biomass responses to nutrient loading treatments all indicated that bacterial growth, fungal growth and respiration were primarily limited by C in both grassland and forest soils. We conclude that enzymatic ratios do not capture the growth-limiting factors for bacterial growth, fungal growth, or respiration in soil. Furthermore, the addition of C-rich plant material could shift the fungal community into N-limitation, while bacteria were shifted into co-limitation by both C and N, revealing that bacteria and fungi can be limited by different nutrients within the same soil environment.

Reforestation accelerates soil organic carbon accumulation: Evidence from microbial biomarkers

Abstract: Soils store more carbon (C) belowground than plants and the atmosphere combined, providing a critical ecosystem service. While previous research has shown that sustainable forest management practices can increase soil C storage by enhancing plant productivity, the role of soil microbes remains elusive. We analyzed changes in plant litter, soil C, and microbial parameters across a reforestation chronosequence—with average stand ages of ∼20, 80, 120, 200 and ≥ 300 years—to evaluate how microbial communities mediate soil C transformation and sequestration. We observed generally consistent increases in microbial biomass (lipid biomarkers), microbial necromass (amino sugar biomarkers), and soil organic C with forest age, highlighting microbial regulation of soil C accumulation. Specifically, increases in microbial biomass preceded gains in soil C, suggesting microbial lipids are an early and sensitive indicator of ecosystem restoration. We also observed a rapid increase in microbial necromass relative to bulk soil C in forests restored for 80–200 years, likely due to accelerated microbial turnover rates. These patterns suggest high plant productivity (low litter C: N ratios) during the early and middle stages of reforestation facilitates efficient microbial growth and necromass accrual in SOC stocks. As forests age, the contribution of microbial necromass to the SOC pool declines toward background levels. Our results suggest reforestation offers a positive feedback solution that mitigates climate change by efficiently sequestering soil C belowground.

Carbon input and allocation by rice into paddy soils: A review

Abstract: Knowledge of belowground C input by rice plants and its fate is essential for managing C cycling and sequestration in paddy soils. Previous reviews have summarized C input and the pathways of root-derived C in upland soils by labeling with 14C or 13C (13/14C), while rice rhizodeposition and C input in paddy soils have not been comprehensively evaluated. Here, we analyzed the results of 13/14C pulse and continuous labeling studies using 112 datasets from 13 articles on the allocation and pathways of photosynthesized C by rice plants to assess C input, budget, and amount stabilized in paddy soils. Overall, 13/14C partitioning estimated by continuous labeling was 72% to the shoots, 17% to the roots, 10% to the soil, and 1.3% was recovered in microbial biomass. Pulse-labeling studies showed a similar C partitioning: 79%, 13%, 5.5%, and 2.1%, respectively. The total belowground C input estimated based on continuous labeling was 1.6 Mg ha−1 after one rice season, of which rhizodeposition accounted for 0.4 Mg C ha−1. Carbon input assessed by pulse labeling was slightly lower (total belowground C input, 1.4 Mg ha−1; rhizodeposition, 0.3 Mg C ha−1; 14 days after labeling). Rice C input after one cropping season was lower than that by upland plants (cereals and grasses, 1.5–2.2 Mg ha−1). In contrast to upland crops, most paddy systems are located in the subtropics and tropics and have two or three cropping seasons per year. We conclude that (1) pulse labeling underestimates the total belowground C input by 15%, compared with that by continuous labeling, and (2) rhizodeposition of rice accounts for approximately 26% of the total belowground C input, regardless of the labeling method used. Based on allocation ratios, we suggest a simple and practical approach for assessment of the gross C input by rice into the soil, for partitioning among pools and for long-term C stabilization in paddies.

Testing the dependence of microbial growth and carbon use efficiency on nitrogen availability, pH, and organic matter quality

Abstract: Microbial carbon use efficiency (CUE), or the partitioning of assimilated C into growth or respiration, is a key parameter that is central to understanding the soil C cycle and its feedback to environmental and climate change. The availability of nitrogen (N), organic matter (OM) quality and environmental factors influence CUE indirectly by affecting growth rates and respiration of the major microbial decomposers in soil, including fungi and bacteria. In the present study we set out to evaluate the effect of N-additions (mineral N fertiliser), increased pH (lime), and increased OM quality (plant litter addition) on microbial growth, respiration, and resulting CUE. We sampled beech and spruce forest stands each including two levels of soil fertility. In laboratory microcosm experiments we then manipulated the availability of mineral N, pH and OM quality during the course of 60 days and measured rates of bacterial and fungal growth, respiration, and resulting CUE. We observed that growth rates of both bacteria and fungi were stimulated by increased OM quality through litter additions, but when combined with increased pH, the ratio shifted in favour of bacteria, while a shift towards fungal dominance was observed when litter was combined with N additions. Overall bacterial growth was stimulated by increased pH and reduced by addition of mineral N, while fungal growth appeared unaffected by both factors. The ratio of fungal to bacterial growth varied between 0.02 and 0.7, suggesting that 0.4 to 50 times more detrital-C was used by bacteria than by fungi in the dataset. Consistently negative correlations between fungal and bacterial growth suggested competitive interactions during the microbial use of detrital C, with bacteria being the dominant competitor. Estimated levels of microbial CUE ranged from <0.05 to 0.5, and higher levels of CUE were associated with higher dominance of bacteria in soils with higher pH and lower N availability. Taken together, differences in CUE were linked to the dominance of fungi or bacteria. When bacterial growth was inhibited by mineral N or low pH, a competitive release resulted in a stimulated fungal growth and detrital C-use, which yielded reduced CUEs. (Less)

Ecoenzymatic stoichiometry and nutrient dynamics along a revegetation chronosequence in the soils of abandoned land and Robinia pseudoacacia plantation on the Loess Plateau, China

Abstract: The effects of vegetation restoration on plant characteristics and soil physicochemical properties have been widely documented; however, knowledge of the variation in soil ecoenzymatic activity and stoichiometry remains limited, particularly with respect to their relationship with plant and soil variables in restored ecosystems. Here, the vegetation and soil from one farmland and two restored land-use types (Robinia pseudoacacia plantations: RP and abandoned lands: AL) of four age classes (10, 18, 28, and 43-years) were investigated and sampled on the Loess Plateau, China. The activity of C, N, and P-acquiring enzymes (β-1,4-glucosidase, BG; β-1,4-N-acetylglucosaminidase, NAG; leucine aminopeptidase, LAP; and alkaline phosphatase, AP) and other major influencing factors (soil physical properties, soil nutrient contents, and microbial biomass) were determined. It was found that both restoration time and vegetation types significantly affect plant characteristics, soil physical properties, soil nutrient content, and microbial biomass. Soil BG, NAG + LAP, and AP enzyme activities were higher in RP and AL than in farmland, and increased with restoration time in AL. For RP, the activity of these enzymes increased from year 10 to year 28, then decreased from year 28 to year 43. Soil ecoenzymatic C:P and N:P activity ratios were ordered: farmland > AL > RP, and decreased with restoration time in AL and RP; thus, P limitation was stronger in RP than in AL and increased with restoration time in both AL and RP. Soil ecoenzymatic C:N:P acquisition ratios of farmland, AL, and RP deviated from the 1:1:1 ratio and depended on the availability of environmental nutrients and demand for microbial nutrients. The vegetation characteristics and soil physical properties were closely related to the nutrient acquisitions of microbes and, ultimately, contributed towards shaping soil ecoenzymatic activity and stoichiometry (particularly vegetation coverage, belowground biomass, soil water content, soil bulk density, and pH). Furthermore, variation in soil ecoenzymatic activity and stoichiometry was better accounted by dissolved nutrients in the soil (particularly C and N) and microbial biomass (particularly N and P) than by plant characteristics and soil properties. Overall, this study demonstrates that the C:N:P stoichiometry of soil microbes and ecoenzymatic activity is nutrient dependent, rather homeostatic, with the potential to influence nutrient cycling on the Loess Plateau.

Impact of long-term agricultural management practices on soil prokaryotic communities

Abstract: The profound intensification of agricultural practices by increased application of agro-chemicals, short crop rotations and ploughing resulted in loss of soil fertility, erosion and accumulation of soil-borne plant pathogens. Soil microbial communities are key players in ecosystem processes and are intimately linked to crop productivity and health. Thus a better understanding of how farming practices affect soil microbiota is needed in order to promote sustainable agriculture. The long-term field trial in Bernburg (Germany) established in 1992 provides a unique opportunity to assess the effects of i) the crop (maize vs. rapeseed) preceding the actual winter wheat culture, ii) tillage practice (mouldboard plough vs. cultivator tillage) and iii) standard nitrogen (N)-fertilization intensity with application of growth regulators and fungicides (intensive) compared to reduced N-fertilization without growth regulators and fungicides (extensive). We hypothesized that these different farming practices affect the soil prokaryotic community structures with consequences for their functional potential. Total community-DNA was extracted directly from soils sampled at wheat harvest. Illumina sequencing of 16S rRNA genes amplified from total community-DNA revealed a significant effect of tillage practice and the preceding crop on prokaryotic community structures, whereas the influence of N-fertilization intensity was marginal. A number of differentially abundant prokaryotic genera and their predicted functions between mouldboard plough vs. cultivator tillage as well as between different preceding crops were identified. Compared to extensive N-fertilization, intensive N-fertilization resulted in higher abundances of bacterial but not of archaeal amoA genes, that are involved in ammonia oxidation. Our data suggest that long-term farming strategies differently shape the soil prokaryotic community structure and functions, which should be considered when evaluating agricultural management strategies regarding their sustainability, soil health and crop performance.

Spatio-temporal microbial community dynamics within soil aggregates.

Abstract: Soil microbial communities are highly spatially organized, shaped in part by the structure of soil itself. Understanding how spatially discrete microbial communities change across years and seasons in response to environmental factors, plant phenology and aggregate turnover, is key to understanding how varying management practices impact the ecology of soil microbial communities. We investigated both seasonal (within year) and annual (across sampling years) changes of discrete microbial communities in soil aggregate fractions, large macroaggregates (LM) and microaggregates (MICRO) in three different bioenergy management systems. We hypothesized that 1) seasonal changes due to plant phenology and aggregate turnover will be most pronounced within the MICRO aggregate soil microbial community; 2) inter-annual variability will lead to changes in microbial diversity across aggregate sizes and the magnitude of change will be mediated by management regime. We found that LM and MICRO aggregates have unique microbial communities within soil. MICRO aggregate microbial communities are more diverse and change more dynamically across the sampling season, peaking in diversity at peak plant growth and maximum biomass. The number of families indicative of specific MICRO aggregate habitats increases over the growing season for both bacteria (from 3 to 51) and fungi (from 8 to 14). The LM aggregates harbored less diverse, yet more stable, communities within a growing season. By contrast, between years the LM aggregates were the most responsive to inter-annual variability. Our study demonstrates the importance of including the spatio-temporal dynamics of soil microbes. We identified “hot spots” of microbial diversity within soil, with a greater diversity of microbes found under prairies, within the MICRO aggregates, and seasonally during peak plant biomass. Targeted analysis of the MICRO aggregates can contribute to deeper understanding of potential diversity and functioning of soil microbial communities for ecosystem maintenance as well as the response to climatic events and environmental change.

Understanding how long-term organic amendments increase soil phosphatase activities: Insight into phoD- and phoC-harboring functional microbial populations

Abstract: In context of the use of organic materials as alternatives for mineral fertilizer, it is important to understand how organic amendments influence soil extracellular phosphatase activities which accelerate the mineralization of organic phosphorus (P). To address this, the current study investigates the influence of organic amendments on acid (ACP) and alkaline (ALP) phosphatase activities in soils and how organic amendments influence these activities from the perspective of microbially-mediated pathways. Herein, a comprehensive meta-analysis of 599 measurements from 106 published studies around the world was performed as well as a field component sourced from a 30-year-old field experiment on fertilization. Based on meta-analysis, organic amendments increased average extracellular ACP and ALP activities by 22% and 53%, respectively, in comparison to the mineral-only fertilization. Observed increases in activities were consistent with significant increases in soil organic carbon (C), total nitrogen (N) and available P contents, and microbial biomass C and N pools. According to the data from the long-term field experiment, we found phoD-harboring species encoding ALP were more closely correlated with phoC-harboring species encoding ACP in organically amended soils, and more network hubs were also observed by organic amendment. Soil C:P and N:P ratios, and microbial biomass C were the main predictors of the abundance, diversity, and composition of the phoC- and phoD-harboring populations. Further analysis revealed that the soil C:P ratio was identified as the dominant predictor of potential ACP and ALP activities. Our work highlights the importance in understanding how soil C:N:P stoichiometry mediates phosphatase-harboring populations in order to determine the downstream consequences of using organic amendments for increasing phosphatase activities.

Carbon and phosphorus addition effects on microbial carbon use efficiency, soil organic matter priming, gross nitrogen mineralization and nitrous oxide emission from soil

Abstract: The quantity and chemical composition of soil organic carbon (C) are primary factors controlling the growth and activity of soil microorganisms However, availability of phosphorus (P) can also limit microbial activity as it is required for the synthesis of genetic and cellular components, metabolism and energy transfer Little is known about how P availability influences microbial activity in response to C of varying chemical composition and recalcitrance A laboratory incubation experiment was conducted to examine the effect of 13C-labeled glucose, oxalic acid and phenol, with and without P, on microbial C use efficiency (CUE), soil organic matter (SOM) priming, gross nitrogen (N) mineralization and nitrous oxide (N2O) emission from a grassland soil Our results showed that microbes used glucose more efficiently but oxalic acid less efficiently compared to more recalcitrant phenol, and did not rely on P nutrition to partition C into growth and respiration All three C substrates caused real SOM priming independent of their energy content or chemical structure, while addition of P increased the priming effect Variability in chemical structures of C substrates affected gross N mineralization and hence N2O emission, while P application directly influenced N2O emission, especially when C substrates were added In conclusion, our findings emphasize that the coupling of C and P fertilization in soils can have strong effects on terrestrial C stocks by favoring native soil organic C loss, as well as on N2O emission

Microbial C:N:P stoichiometry and turnover depend on nutrients availability in soil: A 14C, 15N and 33P triple labelling study

Abstract: Microbial biomass turnover and the associated recycling of carbon (Cmic), nitrogen (Nmic) and phosphorus (Pmic) depend on their stoichiometric relationships and plays a pivotal role for soil fertility. This study examines the responses of Cmic, Nmic, Pmic, the microbial respiration rate (CO2 efflux), and the total DNA content to C and nutrient addition in forest soils with very low (Low-P) and high P (High-P) contents. Both the Low-P and High-P soils were treated with a low and high level of C, N and P (5% and 200% of Cmic, Nmic and Pmic). Phosphorus (33P) was added before the addition of C (14C) and N (15N) to investigate the potential P limitation. We hypothesized two modes of microbial biomass C and nutrient turnover: 1) maintenance through intracellular metabolisms and/or 2) microbial growth and death through necromass reutilization. In Low-P soil, the 2-day-sooner increase of Cmic and Pmic compared to the increase of CO2 efflux and DNA content after high CN input showed the rapid initial uptake of C and limiting nutrients into microbial cells. It also demonstrated a lag period before microbial growth commenced. In High-P soil, however, the CO2 efflux and DNA content increased simultaneously with increases in microbial biomass, reflecting the microbial capacity for immediate growth. Afterwards, CO2 efflux and DNA content dropped to the level before CNP addition, with a decline of Cmic and Pmic in Low-P soil and a decline of Nmic in High-P soil, suggesting a C and P limitation in Low-P soil and N limitation in High-P soil. Under low CNP addition, the microorganisms in High-P soil are ready to grow, while those in Low-P soil are mainly in maintenance mode. The microorganisms under maintenance in low-P soil can switch to growth/death mode after removing the nutrient limitation. High CNP input caused a non-homeostatic response of Cmic: Nmic: Pmic stoichiometry from 691:105:1 to 33:1:1 in Low-P soil, mainly resulting from a higher storage of the limiting elements (C and P) in microbial biomass. The ratio remained stable under low CNP addition due to the endogenous metabolism of C and nutrient at maintenance. The C and nutrient were turnovered much faster by microorganisms in the growth/death mode, confirming a key principle of ecology: the stronger the limitation by an element, the more efficiently that element is retained within an organism, and the more intensively it is reused. The triple labeling approach linked with Cmic: Nmic: Pmic stoichiometry helped to identify the dominant maintenance and growth/death modes of microbial biomass CNP turnover in nutrient-limited and -unlimited soil.

Plant-plant interactions and N fertilization shape soil bacterial and fungal communities

Abstract: The impact of conspecific and heterospecific neighboring plants on soil bacterial and fungal communities has never been explored in a forest ecosystem. In the present study, we first investigated soil microbial communities in three plantations: Larix kaempferi monoculture, L. olgensis monoculture and their mixture. Then, a two-year growth experiment was conducted to investigate the effects of intra- and inter-specific interactions of L. kaempferi and L. olgensis on rhizosphere microbial communities at two different nitrogen levels. The results demonstrated clear differences in the beta-diversity and composition of bacteria and fungi among the three plantations, which implied the presence of different effects of plant-plant interactions on soil microbial communities. The results of the pot experiment showed that L. kaempferi suffered from greater neighbor effects from its conspecific neighbor regardless of N fertilization, although the effect declined when L. kaempferi was grown with L. olgensis under N fertilization. Changes in intra- and inter-specific plant interactions significantly impacted the chemical and biological properties of soil under N fertilization, with lower concentrations of NH4+, and lower soil microbial biomass (CMic) and soil carbon nitrogen biomass (NMic) under intra-specific plant interactions of L. kaempferi (KK) compared to inter-specific interactions of L. kaempferi and L. olgensis (KO). N fertilization increased bacterial and fungal alpha diversities in the rhizosphere soil of KO. For the beta diversity, the PERMANOVA results demonstrated that there was a significant impact of intra- and inter-specific plant interactions on soil microbial communities, with KK significantly differing from intra-specific plant interactions of L. olgensis (OO) and KO. The two plant species and N fertilization showed specific effects on the soil microbial composition, particularly on the fungal community. Both L. olgensis and N fertilization increased the abundance of Ascomycota but reduced that of Basidiomycota, and even shifted the dominance from Basidiomycota to Ascomycota under KO combined with N fertilization.

Diversity of the active phenanthrene degraders in PAH-polluted soil is shaped by ryegrass rhizosphere and root exudates

Abstract: Root exudates can stimulate microbial degradation within the rhizosphere, but their exact roles are embedded within the complicated rhizospheric effects. In the present study, we applied both 12C- and 13C-phenanthrene to distinguish the effects of root exudates within ryegrass rhizosphere on phenanthrene degradation via DNA stable isotope probing (DNA-SIP). A significant increase of phenanthrene biodegradation efficiency (10.7%) was found in ryegrass rhizosphere compared to bulk soils, but not in soils supplemented with ryegrass root exudates. Results from high-throughput sequencing and computational analyses suggested that treatments with both ryegrass rhizosphere and root exudates markedly increased total bacterial populations and shaped the composition of the active phenanthrene-degrader community. Of all the phenanthrene-degraders belonging to eight bacterial classes revealed by DNA-SIP, only Alphaproteobacteria and Nitrososphaeria were shared between bulk soils, ryegrass rhizosphere and soils supplemented with ryegrass root exudates. Sphingobacteriia and Actinobacteria were active phenanthrene-degraders within both ryegrass rhizosphere and soils supplemented with ryegrass root exudates, whereas others were observed only in bulk soils or soils supplemented with ryegrass root exudates. Most of the degraders were linked to phenanthrene degradation for the first time based on their incorporation of 13C-phenanthrene. In 13C-phenanthrene microcosms, the relative abundance of PAH-RHDα genes and active phenanthrene-degraders was strongly correlated with phenanthrene degradation efficiency. Compared to the rhizosphere, root exudates provided a minor contribution to the abundance of PAH-RHDα gene. This study helps in better understanding the roles of root exudates supplement in the phenanthrene biodegradation process within the rhizosphere and provides theoretical insights into the mechanisms of enhanced phenanthrene degradation via phytoremediation at PAH-contaminated sites.

Secondary successional forests undergo tightly-coupled changes in soil microbial community structure and soil organic matter

Abstract: Soil microbes link aboveground and belowground ecosystem processes by modulating nutrient retention, recycling, and availability to plants. The diversity and abundance of soil microbes are influenced by biotic and edaphic factors such as plant communities and soil chemistry. Despite this general understanding, relatively few details are known about how soil microbial community structure responds to changing plant communities and soil chemistry associated with secondary forest succession. To address these gaps, we used 16S rRNA gene sequencing to investigate how diversity, composition and abundance of soil prokaryotic communities differed among five successional stages at two soil depths in a temperate forest, and then related these differences with soil properties. Oligotrophic prokaryotic taxa were more common in earlier successional stages, and community diversity declined at later forest successional stages. Prokaryotic diversity was consistently higher in topsoil than subsoil. Prokaryotic community composition varied with respect to soil organic matter (SOM) properties. The relative abundances of specific carbon (C) functional groups (e.g., aliphatic C groups, aromatic C groups and polysaccharides) revealed by mid-IR spectroscopy were strongly related with prokaryotic community composition. Overall, this study revealed that changes in soil prokaryotic community structure (diversity, composition and taxa abundance) paralleled changes in plant communities and soil chemistry associated with forest succession, and that these changes can be inferred through changes in SOM properties.