Showing papers in "Soil Biology & Biochemistry in 2020"

Rare microbial taxa as the major drivers of ecosystem multifunctionality in long-term fertilized soils

Abstract: Soil microbial communities play an essential role in driving multiple functions (i.e., multifunctionality) that are central to the global biogeochemical cycles. Long-term fertilization has been reported to reduce the soil microbial diversity, however, the impact of fertilization on multifunctionality and its relationship with soil microbial diversity remains poorly understood. We used amplicon sequencing and high-throughput quantitative-PCR array to characterize the microbial community compositions and 70 functional genes in a long-term experimental field station with multiple inorganic and organic fertilization treatments. Compared with inorganic fertilization, the application of organic fertilizer improved the soil multifunctionality, which positively correlated with the both bacterial and fungal diversity. Random Forest regression analysis indicated that rare microbial taxa (e.g. Cyanobacteria and Glomeromycota) rather than the dominant taxa (e.g. Proteobacteria and Ascomycota) were the major drivers of multifunctionality, suggesting that rare taxa had an over-proportional role in biological processes. Therefore, preserving the diversity of soil microbial communities especially the rare microbial taxa could be crucial to the sustainable provision of ecosystem functions in the future.

Do cover crops benefit soil microbiome? A meta-analysis of current research

Abstract: Cover cropping is a promising sustainable agricultural method with the potential to enhance soil health and mitigate consequences of soil degradation. Because cover cropping can form an agroecosystem distinct from that of bare fallow, the soil microbiome is hypothesized to respond to the altered environmental circumstances. Despite the growing number of primary literature sources investigating the relationship between cover cropping and the soil microbiome, there has not been a quantitative research synthesis that is sufficiently comprehensive and specific to this relationship. We conducted a meta-analysis by compiling the results of 60 relevant studies reporting cover cropping effects on soil microbial properties to estimate global effect sizes and explore the current landscape of this topic. Overall, cover cropping significantly increased parameters of soil microbial abundance, activity, and diversity by 27%, 22%, and 2.5% respectively, compared to those of bare fallow. Moreover, cover cropping effect sizes varied by agricultural covariates like cover crop termination or tillage methods. Notably, cover cropping effects were less pronounced under conditions like continental climate, chemical cover crop termination, and conservation tillage. This meta-analysis showed that the soil microbiome can become more robust under cover cropping when properly managed with other agricultural practices. However, more primary research is still needed to control between-study heterogeneity and to more elaborately assess the relationships between cover cropping and the soil microbiome.

A meta-analysis of global cropland soil carbon changes due to cover cropping

Abstract: Including cover crops within agricultural rotations may increase soil organic carbon (SOC). However, contradictory findings generated by on-site experiments make it necessary to perform a comprehensive assessment of interactions between cover crops, environmental and management factors, and changes in SOC. In this study, we collected data from studies that compared agricultural production with and without cover crops, and then analyzed those data using meta-analysis and regression. Our results showed that including cover crops into rotations significantly increased SOC, with an overall mean change of 15.5% (95% confidence interval of 13.8%–17.3%). Whereas medium-textured soils had highest SOC stocks (overall means of 39 Mg ha−1 with and 37 Mg ha−1 without cover crops), fine-textured soils showed the greatest increase in SOC after the inclusion of cover crops (mean change of 39.5%). Coarse-textured (11.4%) and medium-textured soils (10.3%) had comparatively smaller changes in SOC, while soils in temperate climates had greater changes (18.7%) than those in tropical climates (7.2%). Cover crop mixtures resulted in greater increases in SOC compared to mono-species cover crops, and using legumes caused greater SOC increases than grass species. Cover crop biomass positively affected SOC changes while carbon:nitrogen ratio of cover crop biomass was negatively correlated with SOC changes. Cover cropping was associated with significant SOC increases in shallow soils (≤30 cm), but not in subsurface soils (>30 cm). The regression analysis revealed that SOC changes from cover cropping correlated with improvements in soil quality, specifically decreased runoff and erosion and increased mineralizable carbon, mineralizable nitrogen, and soil nitrogen. Soil carbon change was also affected by annual temperature, number of years after start of cover crop usage, latitude, and initial SOC concentrations. Finally, the mean rate of carbon sequestration from cover cropping across all studies was 0.56 Mg ha−1 yr−1. If 15% of current global cropland were to adopt cover crops, this value would translate to 0.16 ± 0.06 Pg of carbon sequestered per year, which is ~1–2% of current fossil fuels emissions. Altogether, these results indicated that the inclusion of cover crops into agricultural rotations can enhance soil carbon concentrations, improve many soil quality parameters, and serve as a potential sink for atmosphere CO2.

Carbon and nitrogen recycling from microbial necromass to cope with C:N stoichiometric imbalance by priming

Abstract: The impact of increasing amounts of labile C input on priming effects (PE) on soil organic matter (SOM) mineralization remains unclear, particularly under anoxic conditions and under high C input common in microbial hotspots. PE and their mechanisms were investigated by a 60-day incubation of three flooded paddy soils amended with13C-labeled glucose equivalent to 50–500% of microbial biomass C (MBC). PE (14–55% of unamended soil) peaked at moderate glucose addition rates (i.e., 50–300% of MBC). Glucose addition above 300% of MBC suppressed SOM mineralization but intensified microbial N acquisition, which contradicted the common PE mechanism of accelerating SOM decomposition for N-supply (frequently termed as “N mining”). Particularly at glucose input rate higher than 3 g kg−1 (i.e., 300–500% of MBC), mineral N content dropped on day 2 close to zero (1.1–2.5 mg N kg−1) because of microbial N immobilization. To cope with the N limitation, microorganisms greatly increased N-acetyl glucosaminidase and leucine aminopeptidase activities, while SOM decomposition decreased. Several discrete peaks of glucose-derived CO2 (contributing >80% to total CO2) were observed between days 13–30 under high glucose input (300–500% of MBC), concurrently with CH4 peaks. Such CO2 dynamics was distinct from the common exponential decay pattern, implicating the recycling and mineralization of 13C-enriched microbial necromass driven by glucose addition. Therefore, N recycling from necromass was hypothesized as a major mechanism to alleviate microbial N deficiency without SOM priming under excess labile C input. Compound-specific 13C-PLFA confirmed the redistribution of glucose-derived C among microbial groups, i.e., necromass recycling. Following glucose input, more than 4/5 of total 13C-PLFA was in the gram-negative and some non-specific bacteria, suggesting these microorganisms as r-strategists capable of rapidly utilizing the most labile C. However, their 13C-PLFA content decreased by 70% after 60 days, probably as a result of death of these r-strategists. On the contrary, the 13C-PLFA in gram-positive bacteria, actinomycetes and fungi (K-strategists) was initially minimal but increased by 0.5–5 folds between days 2 and 60. Consequently, the necromass of dead r-strategists provided a high-quality C–N source to the K-strategists. We conclude that under severe C excess, N recycling from necromass is a much more efficient microbial strategy to cover the acute N demand than N acquisition from the recalcitrant SOM.

Microplastics in the agroecosystem: Are they an emerging threat to the plant-soil system?

Abstract: Despite plastics providing great benefits to our daily life, plastics accumulating in the environment, especially microplastics (MPs; defined as particles

Soil moisture mediates microbial carbon and phosphorus metabolism during vegetation succession in a semiarid region

Abstract: Revegetation of semiarid lands depends upon soil microbial communities to supply nutrients for successive plant species, but microbial activity can be constrained by insufficient water. The objective of this study was to quantify the metabolic limitation of microbes by extracellular enzymatic stoichiometry, and to determine how this affected microbial carbon use efficiency (CUE) with biogeochemical equilibrium model. The study occurred in long-term revegetation experiment with seven successional stages (0, 11, 35, 60, 100, 130 and 150 years) in the Loess Plateau, China. Microbes maintained stoichiometric homeostasis in all successional stages, but plants did not. Microbial metabolism was limited by low soil phosphorus (P) concentration throughout the succession, whereas plants were limited by low soil P during the late successional stages (from 60 to 150 years) only. An increase in soil moisture during succession was associated with greater P limitation in microbes and plants. There was less microbial P limitation at the 35-year successional stage, and the greatest microbial P limitation occurred at the 130-year successional stage. The microbial C limitation followed a unimodal pattern through the vegetation succession and reached a maximum at 100 years of succession (the early forest stage). This coincided with the lowest microbial CUE at 100 years of succession (CUE was from 0.24 to 0.41), suggesting a change in the physiological responses from microbes (such as enzyme synthesis and the priming effect), that tended to reduce soil C sequestration. Our results indicate that soil moisture regulated microbial C and P metabolism during the vegetation succession in this semiarid region, which has implications for understanding how microbial metabolism affects soil C dynamics under vegetation restoration.

The physical structure of soil: Determinant and consequence of trophic interactions

Abstract: Trophic interactions play a vital role in soil functioning and are increasingly considered as important drivers of the soil microbiome and biogeochemical cycles. In the last decade, novel tools to decipher the structure of soil food webs have provided unprecedent advance in describing complex trophic interactions. Yet, the major challenge remains to understand the drivers of the trophic interactions. Evidence suggests that small scale soil physical structure may offer a unifying framework for understanding the nature and patterns of trophic interactions in soils. Here, we review the current knowledge of how restrictions on soil organisms’ ability to sense and access food resources/prey inherent to soil physical structure essentially shape trophic interactions. We focus primarily on organisms unable to deform the soil and create pores themselves, such as bacteria, fungi, protists, nematodes and microarthropods, and consider pore geometry, connectivity and hydration status as main descriptors of the soil physical structure. We point that the soil physical structure appears to mostly limit the sensing and accessibility to food resources/prey, with negative effects on bottom up controls. The main mechanisms are (i) the reduced transport of sensing molecules, notably volatiles, through the soil matrix and (ii) the wide presence of refuges leading to pore size segregation of consumer/predators and food sources/prey in pores of contrasting size. In addition, variations in the connectivity of the soil pores and the water film is suggested as a central aspect driving encounter probability between consumers/predator and food source/prey and hence locally decrease or increase top-down controls. Constraints imposed by the soil physical structure on trophic interactions are thought to be major drivers of the soil diversity and local community assemblage, notably by favoring a variety of adaptations to feed in this dark labyrinth (food specialists/flexible/generalists) and by limiting competitive exclusion through limited encounter probability of consumers. We conclude with possible future ways for an interdisciplinary and more quantitative research merging soil physics and soil food web ecology.

Arbuscular mycorrhiza enhances rhizodeposition and reduces the rhizosphere priming effect on the decomposition of soil organic matter

Abstract: Arbuscular mycorrhizal fungi (AMF) represent an important route for plant carbon (C) inputs into the soil. Nonetheless, the C input via AMF as well as its impact on soil organic matter (SOM) stabilization and C sequestration remains largely unknown. A mycorrhizal wild type progenitor (MYC) and its mycorrhiza defective mutant (reduced mycorrhizal colonization: rmc) of tomato were continuously labeled with 13CO2 to trace root C inputs into the soil and quantify rhizosphere priming effects (RPE) as affected by AMF symbiosis and N fertilization. Mycorrhizal abundance and 13C incorporation into shoots, roots, soil and CO2 were measured at 8, 12 and 16 weeks after transplanting. AMF symbiosis decreased the relative C allocation (% of total assimilated C) to roots, in turn increased the net rhizodeposition. Positive RPE was recorded for both MYC and rmc plants, ranging from 16–71% and 25–101% of the unplanted control, respectively. Although net rhizodeposition was higher for MYC than rmc plants 16 weeks after transplanting, the RPE was comparatively lower. This indicated a higher potential for C sequestration by plants colonized with AMF (MYC) because the reduced nutrient availability restricts the activity of free-living decomposers. Although N fertilization decreased the relative C allocation to roots, rhizosphere and bulk soil, it had no effect on the absolute amount of rhizodeposition to the soil. The RPE and N-cycling enzyme activities decreased by N fertilization 8 and 12 weeks after transplanting, suggesting a lower microbial N demand from SOM mining. The positive relationship between enzyme activities involved in C cycling, microbial biomass C and SOM decomposition underlines the microbial activation hypothesis, which explains the RPE. We therefore concluded that AMF symbiosis and N fertilization increase C sequestration in soil not only by increasing root C inputs, but also by lowering native SOM decomposition and RPE.

Nutrient addition reduces carbon sequestration in a Tibetan grassland soil: Disentangling microbial and physical controls

Abstract: Nitrogen (N) and phosphorus (P) availability strongly affects carbon (C) cycling and storage in terrestrial ecosystems. Nutrient addition can increase C inputs into soil via increased above- and belowground plant productivity, but at the same time can accelerate organic matter decomposition in the soil. The mechanisms underlying these effects on soil organic C (SOC) dynamics remain unclear, especially in nutrient-limited alpine ecosystems that have been subjected to increasing N and P availability in recent decades. The aim of this study was to clarify the mechanisms underlying SOC decomposition and stabilization in an alpine grassland soil after four years of N and P additions. The soil aggregate size distribution, microbial community structure (lipid biomarkers), microbial C use efficiency (CUE) and microbial necromass composition (amino sugar biomarkers) were analyzed. Nutrient addition increased dominance of fast-growing bacteria (copiotrophs), while P addition alone intensified the competitive interactions between arbuscular mycorrhizal and saprotrophic fungi. These changes led to decreases in the microbial CUE of glucose by 1.6–3.5% and of vanillin by 8.5%, and therefore, reduced SOC content in the topsoil. The total microbial necromass remained unaffected by nutrient addition, but the contribution of fungal necromass to SOC increased. The increased abundance of arbuscular mycorrhizal fungi and fungal necromass under elevated N availability raised the mass proportion of soil macroaggregates (>250 μm) by 16.5–20.3%. Therefore, fungi were highly involved in macroaggregation following N addition, and so, moderated the SOC losses through enhanced physical protection. Overall, the complex interactions between microbial physiology (CUE), necromass composition (amino sugars) and physical protection (macroaggregation) in mediating SOC dynamics in response to nutrient enrichment were disentangled to better predict the capability of alpine grassland soils to act as a C sink or source under global change.

Farmyard manure applications stimulate soil carbon and nitrogen cycling by boosting microbial biomass rather than changing its community composition

Abstract: Land application of farmyard manure (FYM) is a widespread agronomic practice used to enhance soil fertility, but its long-term effects on soil microbial carbon (C) and nitrogen (N) cycling have not been investigated in detail. Topsoils (0–23 cm) and subsoils (23–38 cm) were collected from a field trial on a sandy-textured soil where FYM had been applied at high (50–25 t ha−1 yr−1, 28 yr) and low rates (10 t ha−1 yr−1, 16 yr), and compared to soil treated only with synthetic NPK fertilisers. The turnover rate of key components of soil organic matter (SOM; proteins, peptides, amino acids, cellulose, and glucose) were evaluated by 14C labelling and measuring cellobiohydrolase, β-glucosidase, β-1,4-N-acetylglucosaminidase, L-leucine aminopeptidase, protease, and deaminase activities, whereas gross NH4+ and NO3− production and consumption were determined by 15N-isotope pool dilution. Microbial communities were determined using phospholipid fatty acid (PLFA) profiling. Our results indicate that long-term FYM addition significantly enhanced the accumulation of soil C and N, soil organic N (SON) turnover, exoenzyme activity, and gross NO3− production and assimilation. Rates of protein, peptide, and amino acid processing rate were 169–248, 87–147, and 85–305 mg N kgDWsoil−1 d−1, respectively, gross NH4+ and NO3− production and consumption were 1.8–5.8 mg N kgDWsoil−1 d−1, and the highest rates were shown under the high FYM treatment in topsoil and subsoil. The half-life of cellulose and glucose decomposition under the high FYM treatment were 16.4% and 31.0% lower than them in the synthetic NPK fertiliser treatment, respectively, indicating higher rates of C cycling under high manure application as also evidenced by the higher rate of CO2 production. This was ascribed to an increase in microbial biomass rather than a change in microbial community structure. Based on the high pool sizes and high turnover rate, this suggests that peptides may represent one of the dominant forms of N taken up by soil microorganisms. We conclude that long-term FYM application builds SOM reserves and induces faster rates of nutrient cycling by boosting microbial biomass rather than by changing its community composition.

Soil extracellular enzyme stoichiometry reflects the shift from P- to N-limitation of microorganisms with grassland restoration

Abstract: Soil extracellular enzyme stoichiometry (EES), the ratio of extracellular enzyme activities (EEAs) related to the acquisition of nutrients such as carbon (C), nitrogen (N) and phosphorus (P), reflects the demand for resources by microorganisms. However, how grassland restoration shifts microbial nutrient limitation as indicated by soil EES remains unclear. Here, we evaluated microbial nutrient limitation by studying soil EES across a chronosequence of grassland restoration sites. The ratio of the natural logarithm of C-, N-, and P-acquiring enzymes in our studied system ranged from 1:1.47:1.05 to 1:0.82:1.38, and the average was 1:1.08:1.28, deviating from the global ratio of 1:1:1 and indicating that microorganisms were co-limited by N and P. Enzyme N:P ratio increased and vector angles decreased with time since restoration, suggesting that the restored grassland shifted from P-limitation (angles>45°) to N-limitation (angles

Effects of nitrogen and phosphorus addition on microbial community composition and element cycling in a grassland soil

Abstract: Microorganisms mediate nutrient cycling in soils, and thus it is assumed that they largely control responses of terrestrial ecosystems to anthropogenic nutrient inputs. Therefore, it is important to understand how increased nitrogen (N) and phosphorus (P) availabilities, first, affect soil prokaryotic and fungal community composition and second, if and how changes in the community composition affect soil element cycling. We measured soil microbial communities and soil element cycling processes along a nine-year old experimental N-addition gradient partially crossed with a P-addition treatment in a temperate grassland. Nitrogen addition affected microbial community composition, and prokaryotic communities were less sensitive to N addition than fungal communities. P addition only marginally affected microbial community composition, indicating that P is less selective than N for microbial taxa in this grassland. Soil pH and total organic carbon (C) concentration were the main factors associated with prokaryotic community composition, while the dissolved organic C-to-dissolved N ratio was the predominant driver of fungal community composition. Against our expectation, plant biomass and plant community structure only explained a small proportion of the microbial community composition. Although microbial community composition changed with nutrient addition, microbial biomass concentrations and respiration rates did not change, indicating functional redundancy of the microbial community. Microbial respiration, net N mineralization, and non-symbiotic N2 fixation were more strongly controlled by abiotic factors than by plant biomass, plant community structure or microbial community, showing that community shifts under increasing nutrient inputs may not necessarily be reflected in element cycling rates. This study suggests that atmospheric N deposition may impact the composition of fungi more than of prokaryotes and that nutrient inputs act directly on element-cycling rates as opposed to being mediated through shifts in plant or microbial community composition.

Similar drivers but different effects lead to distinct ecological patterns of soil bacterial and archaeal communities

Abstract: Bacteria and archaea play important roles in soil biogeochemical cycles and the health of terrestrial organisms. They usually coexist in various soil habitats; however, the ecological patterns of bacteria and archaea in the same soil habitats still remain unclear. Here, we compared the community features of the two domains in bulk soils under different vegetation covers. Generally, both bacterial abundance and α-diversity were higher than those of archaea, and the differences were more noticeable in agricultural soils than in non-agricultural saline soils. Compared with bacteria, the archaeal community showed more niche limitation with less widely distributed taxa. Interestingly, similar edaphic factors were correlated with both bacteria and archaea but with opposite effects, of which salinity was the most important driving factor. With the rise of salinity, bacterial α-diversity and abundance decreased, but archaeal diversity increased. Majority of the dominant bacterial taxa showed significantly negative correlation with salinity, such as Alphaproteobacteria, Betaproteobacteria, Acidobacteria and Nitrospirae. In contrast, except Thaumarchaeota, most archaeal predominant taxa from Euryarchaeota, Woesearchaeota and Nanohaloarchaeota were positively related to salinity. Furthermore, network analyses showed that not only bacteria but also considerable archaea-related nodes, edges and potential keystone taxa existed in the networks, especially in saline soils, indicating that archaea also had important positions in microbial co-occurrence networks. These results extended our understanding on the ecological patterns of prokaryotes in terrestrial ecosystems.

Network analysis reveals the strengthening of microbial interaction in biological soil crust development in the Mu Us Sandy Land, northwestern China

Abstract: Although studies examining changes in the structure and diversity of microbial communities in biological soil crusts (BSCs) have increased, microbial interactions in BSCs are not currently fully understood. In this study, we applied a random matrix theory (RMT)-based network approach to construct bacterial, fungal and bacteria-fungal interaction networks for the four developmental stages of BSCs (bare sand, physical crusts, algae crusts and moss crusts) in the Mu Us Sandy Land, northwestern China. Our results showed that Firmicutes, Proteobacteria, Cyanobacteria and Actinobacteria were the keystone phylum in bacterial networks in the four developmental stages, respectively. Ascomycota was the keystone phylum in the fungal networks in all stages, and Basidiomycota was a further keystone phylum in the algae and moss crust networks. With the development of BSCs, complexity in bacterial and fungal networks increased, becoming more clustered and connected, indicating a strengthened pattern in microbial interactions with BSC development. Positive links dominated in all networks, showing that microbial synergism was important in the development of BSCs. Interestingly, with the development of BSCs, the proportion of negative links in bacterial networks increased and they decreased in fungal networks, suggesting more inter-community competition was present in the bacterial communities and less inter-community competition was present in the fungal communities. Environmental factors, especially total carbon and total organic carbon, constrained most bacterial and fungal communities, respectively. Our findings provided a new insight into understanding BSC developmental mechanisms and ecological functions in a desert ecosystem composed of a sandy land landscape in arid and semi-arid regions.

Deliberate introduction of invisible invaders: A critical appraisal of the impact of microbial inoculants on soil microbial communities

Abstract: Non-target effects of deliberately released organisms into a new environment are of great concern due to their potential impact on the biodiversity and functioning of ecosystems Whereas these studies often focus on invasive species of macro-organisms, the use of microbial inoculants is often expected to have specific effects on particular functions but negligible overall effects on resident microbial communities Here, we posit that such introductions often impact native microbial communities, which might influence ecosystem processes Focusing on soil communities, we used a literature search to examine the impact of microbial inoculation (often the release of beneficial microorganisms in agricultural systems) on resident microbial communities Of 108 studies analyzed, 86% showed that inoculants modify soil microbial communities in the short or long term In addition, for studies analyzing the consequences of microbial inoculants in the longer term, 80% did not observe the resilience (return to the initial state) of the resident community following inoculation Through the knowledge gathered from each study, we propose a synthetic and mechanistic framework explaining how inoculants may alter resident microbial communities We also identify challenges as well as future approaches to shed more light on this unseen reality

Soil microbial diversity and composition: Links to soil texture and associated properties

Abstract: Soil texture is an essential component of soil survey for estimating potentials and limitations of land use and management. It has been appreciated as an important predictor for numerous soil processes. However, its connections with the diversity and composition of the soil microbial community remain less understood. This work employed a marker gene high-throughput sequencing approach to determine soil texture-based patterns of bacterial and fungal distribution. Thirty-six intact soil cores were sampled from bermudagrass ecosystems across seven soil texture classes with sand fraction varying from 30.3 to 83.4% and clay fraction from 4.4 to 53.0%. These soil cores were arranged into three sets of equal numbers, and each set of 12 was subjected to three moisture regimes (dry spell, field moisture, and saturation-field capacity), respectively, for 15 days. Soil cores were further stratified into top and bottom sections, leading to a total of 72 samples with varying soil physical and chemical properties. Our data revealed that fungal alpha diversity was more strongly related to soil texture than bacterial alpha diversity, with fungal species richness and Shannon diversity being positively correlated with the sand fraction. Soil texture was the second most important factor after soil pH in shaping the soil microbial community. Relative abundances of some fungi (Basidiomycota and Eurotiomycetes) and filamentous bacteria (Actinobacteria, Chloroflexi) significantly increased with silt and/or clay content. The genetic potential for the degradation of organic compounds also appeared to be higher in finer textured soils than the coarse-textured soils. By identifying sand, silt or clay-preferred microbial taxa and characterizing mineral particle-dependent genetic potential of organic carbon degradation and nitrogen cycling, this work highlighted the significance of soil texture and texture-associated pores, and resource locality, in regulating microbial diversity and community composition.

Long-term high-P fertilizer input decreased the total bacterial diversity but not phoD-harboring bacteria in wheat rhizosphere soil with available-P deficiency

Abstract: Appling phosphorus (P) fertilizer to agroecosystems affects not only crop yield but also associated soil microbial communities. The bacterial phoD gene encodes alkaline phosphatase (ALP) and plays an important role in organic P decomposition in soils. However, the impacts of long-term P fertilization on the bacterial phoD gene community, the total bacterial community, and the relationships of these communities with soil properties are poorly understood in loess soils with available-P deficiency. In this study, the impact of mineral P fertilization on the soil bacterial community was assessed. The 16S rRNA and phoD genes were targeted in DNA extracted from wheat rhizosphere soils subjected to five P fertilization rates (0 (P0), 50 (P50), 100 (P100), 150 (P150) and 200 (P200) kg P2O5 ha−1 yr−1) applied annually for 14 years. Compared to the P0 treatment, the P fertilization treatments increased the soil organic C (SOC), microbial biomass C (MBC) and available P (AP), and in the high-P treatments (P150 and P200) the total P (TP) and organic P (OP) increased, while the ALP activity decreased. All P fertilization treatments reduced the total bacterial diversity (Shannon index). However, only P200 decreased the number of operational taxonomic units (OTUs) with the 16S rRNA gene, and no P fertilization treatments affected phoD-harboring bacterial OTUs or diversity when compared to those in the P0 treatment. Additionally, compared to P0, the P fertilization treatments changed the 16S rRNA and phoD gene bacterial community compositions, with increased relative abundances of 3 phyla and 7 genera and decreased abundances of 1 phylum and 2 genera for the 16S rRNA gene and increased abundances of 4 genera and decreased abundances of 2 phyla and 1 genus for the phoD gene. Microbial network analysis showed that the high-P treatments (P150 and P200) reduced the number of links in the microbial network at the genus level for the 16S rRNA gene. Principal coordinate analysis (PCoA) showed that P fertilization treatments shifted the total bacterial community structure, and redundancy analysis (RDA) revealed that soil dissolved organic C (DOC) and P (AP, OP, TP and ALP) levels were significantly related to the total bacterial community structure. In conclusion, this study demonstrated that long-term P fertilization significantly affected soil C and P as well as the total and phoD-harboring bacterial community compositions in wheat rhizosphere soils and that high P fertilizer application rates reduced total bacterial OTUs, diversity and the connections, which might affect soil biogeochemical cycles.

Soil microbial community responses to labile organic carbon fractions in relation to soil type and land use along a climate gradient

Abstract: Comision Nacional de Investigacion Cientifica y Tecnologica (CONICYT) CONICYT FONDECYT 1161045 1150171 CONICYT Doctorado Nacional Scholarship, Government of Chile 21140873 Comision Nacional de Investigacion Cientifica y Tecnologica (CONICYT) CONICYT FONDECYT 3160424

Microbial growth and enzyme kinetics in rhizosphere hotspots are modulated by soil organics and nutrient availability

Abstract: The input of labile organics by plant roots stimulates microbial activity and therefore facilitates biochemical process rates in the rhizosphere compared to bulk soil, forming microbial hotspots. However, the extent to which the functional properties of soil microorganisms are different in the hotspots formed in soils with contrasting fertility remains unclear. We identified the hotspots related to different levels of Zea mays L. root architecture by zymography of leucine aminopeptidase in two soils with contrasting fertility. The hotspots localized by tiny wet-needle approach around first- and second-order roots were compared for parameters of microbial growth and enzyme kinetics. The pattern of hotspot distribution was more dispersed and the hotspot area was one order of magnitude smaller around first-versus second-order roots. The specific microbial growth rate (μm) and biomass of active microorganisms were soil-specific, with no difference between the hotspots and bulk soil in the fertile soil. In contrast, in the soil poor in organic matter and nutrients, 1.2-fold higher μm and greater growing biomass were found in the hotspots versus bulk soil. Lower enzyme affinity (1.3–2.2 times higher Km value) of β-glucosidase and leucine aminopeptidase to the substrate was detected in the hotspots versus bulk soil, whereas only β-glucosidase showed higher potential enzyme activity (Vmax) in the hotspots, being 1.7–2.1 times greater than that in bulk soil. Notably, the activity of C-acquiring enzyme, β-glucosidase positively correlated with the biomass of actively growing microorganisms. The fertile soil, on the whole, showed greater Vmax and catalytic efficiency (Vmax/Km) and an approximately 2.5 times shorter substrate turnover time as compared to the poor soil. Therefore, we conclude that i) the differences in microbial growth strategy between rhizosphere hotspots and bulk soil were dependent on soil fertility; ii) affinity of hydrolytic enzyme systems to substrate was mainly modulated by plant, whereas potential enzymatic activity was driven by both plant and soil quality.

Direct measurement of the in situ decomposition of microbial-derived soil organic matter

Abstract: Soil organic matter (SOM) is the dominant reservoir of terrestrial organic carbon and nitrogen, and microbial necromass represents a primary input to it. However, knowledge of stabilization mechanisms and direct measurements of the decomposition of microbial-derived SOM are lacking. Here we report a novel 15N isotope pool dilution approach using labeled amino sugars and muropeptides as tracers to quantify the decomposition of proteins and microbial cell walls, which allows to estimate in situ decomposition rates of microbial-derived SOM. Our results demonstrate that microbial cell walls are as recalcitrant as soil protein, exhibiting comparable turnover times across various ecosystems. The bacterial peptidoglycan in soils was primarily decomposed to muropeptides which can be directly utilized by microbes without being further depolymerized to free amino compounds. Moreover, bacterial peptidoglycan decomposition was correlated with soil microbial biomass while fungal chitin and soil protein decomposition were correlated with high soil pH and fine soil texture. This approach thereby provides new insights into the decomposition pathways and stabilization mechanisms of microbial-derived SOM constituents pertaining to SOM persistence.

Rewetting of soil: Revisiting the origin of soil CO2 emissions

Abstract: Rewetting dry soils is associated with a burst of microbial activity and mineralization, which manifests itself as a pulse in soil CO2 emissions, long-known as the Birch effect. In arid and semi-arid systems, soil CO2 losses upon rewetting at the end of extended dry periods can contribute a significant fraction to the overall carbon (C) budget. Microbial biomass is one of the sources of mineralized C, as was demonstrated over 30 years ago (Kieft et al., 1987). The present paper offers a perspective on how the field has progressed since the 1987 paper was published in Soil Biology & Biochemistry, what it means in terms of current concerns about global climate change, and the needs and potential emphases of future research. Many studies since 1987 have addressed the origin of this CO2 pulse, finding multiple possible C sources involving both biotic and abiotic processes. We propose that the magnitude of the rewetting event (Δψ) determines the relative contribution from the array of substrates that contribute to the soil CO2 pulse upon rewetting. The magnitude of the CO2 pulse is likely related to soil physical characteristics and to the size of the available C pool, which is partly controlled by plants. Further, the relative contributions of the mechanisms generating soil CO2 pulses upon rewetting are likely to be modified by climate change. To understand and predict the magnitude of soil CO2 pulses upon rewetting, we advocate continued cross-disciplinary research involving soil microbial ecology, soil physics, soil chemistry, as well as increased integration and recognition of the importance of plant-soil interactions in controlling the soil C pools contributing to soil CO2 pulses.

Soil microbial carbon and nutrient constraints are driven more by climate and soil physicochemical properties than by nutrient addition in forest ecosystems

Abstract: Soil enzymes produced by microorganisms transform substrates in the soil carbon (C) and nutrient cycles. Limitations in C and other nutrients could affect microbial biosynthesis processes, so we expect that soil enzyme activity will reflect microbial deficiencies in C, nitrogen (N) and phosphorus (P) at a large spatial scale. We collected soil from nutrient addition trials in eight forest ecosystems, ranging from temperate forests to tropical forests in eastern China, and conducted vector analysis of the soil enzymatic stoichiometry to examine the spatial extent of soil microbial C and nutrient limitations. We also determined whether nutrient addition could alleviate nutrient limitation or otherwise impact soil microbial resource use. Soil microbial C vs. nutrient limitation (thereafter C limitation) was greater in the temperate forests than in the tropical forests, but did not vary with soil depth. Soil microbial P vs. N limitation (thereafter nutrient limitation) decreased with latitude, and increased with soil depth. We found a negative relationship between soil microbial C limitation and nutrient limitation, which was more pronounced in the topsoil than in deeper soil depths. Furthermore, we found that climate (mean annual precipitation and temperature), soil pH and soil nutrients were significantly correlated with soil microbial C (explaining about 23% of the variation) and nutrient limitation (responsible for about 87% of the variation). Nutrient addition represented ~1% of the variation in soil microbial C and nutrient limitations and thus did not alleviate nutrient deficiencies. We conclude that soil microbial C and nutrient limitations are more likely driven by climate and soil physicochemical properties than by nutrient addition in eight forest ecosystems. Since soil microbial C and nutrient limitations result from long-term adaptation of soil microbial communities to site-specific soil and environmental conditions, the soil enzyme activity is not modified by short-term changes in nutrient availability resulting from fertilizer application.

Nitrogen addition has contrasting effects on particulate and mineral-associated soil organic carbon in a subtropical forest

Abstract: Increasing atmospheric nitrogen (N) deposition has substantially affected carbon (C) and nutrient cycling in forest ecosystems. However, the responses of different soil organic carbon (SOC) fractions with different turnover rates to N addition are highly divergent, and the underlying mechanisms remain elusive. In this study, we explored the responses of surface soil (0–10 cm) characteristics and microbial communities to six years of experimental N addition (0, 50, 100 and 150 kg N ha−1 yr−1) in a subtropical evergreen broadleaf forest in southern China. Our results showed that N addition led to significant soil acidification (pH from 5.3 to 4.9). Microbial biomass carbon and total microbial, bacterial and fungal abundance (phospholipid fatty acid, PLFA) were reduced by N addition, but extracellular enzymes involved in C, N and phosphorus (P) cycling were not responsive to N addition. Soil extractable Ca2+ concentration was depleted by N addition, while other extractable cations (Fe3+, Al3+, Mg2+, K+, Na+) were not affected. Moreover, N addition did not significantly change the C and N concentration of bulk soil. We further separated the bulk soil into particulate organic matter (>53 μm, POM) and mineral-associated organic matter (

Does ecoenzymatic stoichiometry really determine microbial nutrient limitations

Abstract: Recently, an increasing number of studies use ecoenzymatic stoichiometry for determining nutritional status or nutrient limitations of microbes. According to the ecoenzymatic stoichiometry theory, the ratios of β-1,4-glucosidase (BG) and β-1,4-N-acetylglucosaminidase (NAG) (BG:NAG) or BG and NAG + leucine aminopeptidase (LAP) (BG:(BG + LAP)) reflect microbial carbon (C) vs nitrogen (N) limitation, with larger ratios indicating C limitation. However, several studies reported that the ratios did not reflect the C vs N limitations. In this paper, I propose a new conceptual model to distinguish when BG:NAG (or BG:(BG + NAG)) reflects microbial C vs N limitation and when not: If cellulose is a predominant C source (relative to chitin, peptidoglycan, and protein), BG:NAG (or BG:(BG + NAG)) reflects the C vs N limitation as the enzymatic stoichiometry theory suggests, while if chitin, peptidoglycan, and protein are dominant C sources, C vs N limitation cannot be determined by BG:NAG (or BG:(BG + NAG)).

Rusty sink of rhizodeposits and associated keystone microbiomes

Abstract: Iron hydroxides serve as an efficient ‘rusty sink’ promoting the stabilization of rhizodeposits into soil organic carbon (SOC). Our work aimed to understand the physicochemical and microbial mechanisms promoting rhizodeposit (rhizo-C) stabilization as influenced by goethite (α-FeOOH) or nitrogen (N), using 13C natural abundance methodologies and DNA sequencing, in the rhizosphere of maize (Zea mays L.). The addition of N fertilizer to soil increased the mineralization of both rhizo-C and SOC, while amendment with α-FeOOH decreased rhizo-C derived CO2 and lowered the rhizosphere priming effect by 0.57 and 0.74-fold, respectively, compared to the control soil. This decrease resulted from the co-precipitation of rhizo-C at the reactive α-FeOOH surfaces as Fe-organic matter complexes (FeOM), which was 10-times greater than the co-precipitation on short-range ordered minerals. The highest portion of rhizo-C (67% of the total accumulated in soil) was protected within macroaggregates (>2 mm). Carbon overlapped with α-FeOOH mainly in >2 mm aggregates, as shown by HRTEM-EDS imaging, suggesting that α-FeOOH associated rhizo-C stimulated aggregate formation. Random forest analysis confirmed that the stabilization of rhizo-C was controlled mainly by physiochemical binding within FeOM complexes and macroaggregates. Rhizo-C mineralization was regulated by the keystone microbiome: Paucimonas (β-Proteobacteria) being an r-strategist with rapid growth under soil without nutrient limitation (N treated) and Steroidobacter (Actinobacteria) with branched filaments that can access C and nutrients under oligotrophic conditions (goethite enriched soil). Two-way orthogonal partial least squares analysis revealed that the rhizosphere priming effect was facilitated mainly by the same genera, most likely due to co-metabolism. The genera belonging to Acidimicrobiaceae (Actinobacteria), Cryptococcus and Cystofilobasidium (Basidiomycota) were positively correlated with the accumulation of rhizo-C in the >2 mm aggregate size, which might due to their high affinity towards α-FeOOH and contribution to the development of aggregation via filamentary structures that interact with microaggregates. We suggest that rhizodeposit stabilization in soil was balanced by microbial mineralization and abiotic associations with the “rusty sink” and organisms with branched filaments contributing to the development of aggregation.

Prevalent root-derived phenolics drive shifts in microbial community composition and prime decomposition in forest soil

Abstract: Phenolic compounds perform various functions in soil ranging from microbial substrate to toxin and form the basis of several plant-mediated processes. The aim of this study was to investigate how phenolics commonly exuded by tree roots influence soil organic matter (SOM) decomposition and interact with other labile forms of carbon (C) abundant in root exudates. Therefore, we performed a 38-day incubation experiment and assessed whether phenolic compounds (benzoic acid, caffeic acid and catechin) facilitated or inhibited SOM decomposition in a glucose-amended forest soil. Changes in decomposition, substrate use, fungal and bacterial community composition, and microbial abundance and activity were measured over time using 13C-stable-isotope tracing, DNA-based molecular methods and enzyme assays. Our findings showed that phenolics inhibited microbial activity and abundance to varying degrees. Yet, benzoic acid was the only compound producing a substantial priming effect leading to a 21% increase in SOM decomposition, which was amplified in glucose-amended soils. This stimulation in microbial activity was associated with an increase in β-1,4-glucosidase activity and the bacterial genera Paraburkholderia and Caballeronia of the Burkholderiaceae family. Phenolics drove microbial community shifts in glucose-amended soils with negligible interactive effects. In conclusion, phenolic priming of SOM decomposition is associated with microbial community shifts and amplified in the presence of glucose. This evidence emphasizes the need for considering phenolics and interactions among root exudates as priming mechanisms in the rhizosphere and other soil environments where aromatics and phenolic compounds are abundant.

Soil properties rather than climate and ecosystem type control the vertical variations of soil organic carbon, microbial carbon, and microbial quotient

Abstract: Small changes in soil organic carbon (SOC) may have great influences on the climate-carbon (C) cycling feedback However, there are large uncertainties in predicting the dynamics of SOC in soil profiles at the global scale, especially on the role of soil microbial biomass in regulating the vertical distribution of SOC Here, we developed a database of soil microbial biomass carbon (SMBC), SOC, and soil microbial quotient (SMQ = SMBC/SOC) from 289 soil profiles globally, as well as climate, ecosystem types, and edaphic factors associated with these soil profiles We assessed the vertical distribution patterns of SMBC and SMQ and the contributions of climate, ecosystem type, and edaphic condition to their vertical patterns Our results showed that SMBC and SMQ decreased exponentially with soil depth, especially within the 0–40 cm soil depth SOC also decreased exponentially with depth but in different magnitudes compared to SMBC and SMQ Edaphic factors (eg, soil clay content and C/N ratio) had the strongest control on the vertical distributions of SMBC and SMQ, probably by mediating substrate and nutrient supplies for microbial growth in soils Mean annual temperature and ecosystem types (ie, forests, grasslands, and croplands) had weak influences on SMBC and SMQ In contrast, the vertical distribution of SOC was significantly affected by climate and edaphic factors Climate and ecosystem types likely simultaneously affected multiple factors that control SMBC, such as the distribution of soil clay and nutrients along soil profiles Overall, our data synthesis provides quantitative information of how SMBC, SMQ, and SOC changed along soil profiles at large spatial scales and identifies important factors that influence their vertical distributions The findings can help improve the prediction of C cycling in terrestrial ecosystems by incorporating the contribution of soil microbes in Earth system models

Application of biofertilizer containing Bacillus subtilis reduced the nitrogen loss in agricultural soil

Abstract: Nitrogen losses caused by excess fertilizer application in agriculture are one of the main sources of non-point pollution. Biofertilizer has been considered as an effective alternative to synthetic nitrogen fertilizer, but the effectiveness and mechanism for controlling non-point pollution remains unclear. In this study, the effect of biofertilizer containing Bacillus subtilis on nitrogen loss in agricultural soil was investigated. Compared with the application of urea alone, the strategy of substituting 50% urea with biofertilizer reduced the nitrogen loss from farmland soil by 54%. Moreover, this strategy also increased nitrogen use efficiency by 11.2% and achieved a 5.0% increase in crop yield. Application of biofertilizer decreased the abundance of bacterial amoA gene and increased the abundance of narG, nirS, nirK, and nosZ genes in soil. This implied a decrease in nitrification and an increase in denitrification. Thus, it reduced the accumulation of NO3−-N in soil and greatly reduced nitrogen runoff and leaching loss. In addition, biofertilizer decreased the abundance of nitrogen-fixing gene nifH by up to 2 times. Application of biofertilizer also increased the abundance of Bacteroidetes and Chloroflexi, which play important roles in degradation of soil organic matter. In conclusion, the biofertilizer regulated the microbial nitrogen transformation process in soil and reduced nitrogen loss from agroecosystems.

Anaerobic oxidation of methane in paddy soil: Role of electron acceptors and fertilization in mitigating CH4 fluxes

Abstract: The anaerobic oxidation of methane (AOM) in marine ecosystems is ubiquitous and largely coupled to sulfate reduction. In contrast, the role of AOM in terrestrial environments and the dominant electron acceptors driving terrestrial AOM needs deeper understanding. Submerged rice paddies with intensive CH4 production have a high potential for AOM, which can be important for greenhouse gas mitigation strategies. Here, we used 13CH4 to quantify the AOM rates in paddy soils under organic (Pig manure, Biochar) and mineral (NPK) fertilization. Alternative-to-oxygen electron acceptors for CH4 oxidation, including Fe3+, NO3−, SO42−, and humic acids, were examined and their potential for CH4 mitigation from rice paddies was assessed by 13CH4 oxidation to 13CO2 under anoxic conditions. During 84 days of anaerobic incubation, the cumulative AOM (13CH4-derived CO2) reached 0.15–1.3 μg C g-1 dry soil depending on fertilization. NO3- was the most effective electron acceptor, yielding an AOM rate of 0.80 ng C g-1 dry soil h-1 under Pig manure. The role of Fe3+ in AOM remained unclear, whereas SO42- inhibited AOM but strongly stimulated the production of unlabeled CO2, indicating intensive sulfate-induced decomposition of organic matter. Humic acids were the second most effective electron acceptor for AOM, but increased methanogenesis by 5–6 times in all fertilization treatments. We demonstrated for the first time that organic electron acceptors (humic acids) are among the key AOM drivers and are crucial in paddy soils. The most pronounced AOM in paddy soils occurred under Pig manure, followed by Control and NPK, while AOM was the lowest under Biochar. We estimate that nitrate (nitrite)-dependent AOM in paddy fields globally consumes ~3.9 Tg C–CH4 yr-1, thereby offsetting the global CH4 emissions by ~10–20%. Thus, from a broader agroecological perspective, the organic and mineral fertilizers control an important CH4 sink under anaerobic conditions in submerged ecosystems. Appropriate adjustments of soil fertilization management strategies would therefore help to decrease the net CH4 flux to the atmosphere and hence the global warming.

The soil priming effect: Consistent across ecosystems, elusive mechanisms

Abstract: Organic matter input to soils can accelerate the decomposition of native soil carbon (C), a process called the priming effect. Priming is ubiquitous and exhibits some consistent patterns, but a general explanation remains elusive, in part because of variation in the response across different ecosystems, and because of a diversity of proposed mechanisms, including microbial activation, stoichiometry, and community shifts. Here, we conducted five-week incubations of four soils (grassland, pinon-juniper, ponderosa pine, mixed conifer), varying the amount of substrate added (as 13C-glucose, either 350 or 1000 μg C g−1 week−1) and either with no added nitrogen (N), or with sufficient N (as NH4NO3) to bring the C-to-N ratio of the added substrate to 10. Using four different ecosystems enabled testing the generality of mechanisms underlying the priming effect. The responses of priming to the amount and C-to-N ratio of the added substrate were consistent across ecosystems: priming increased with the rate of substrate addition and declined when the C-to-N ratio of the substrate was reduced. However, structural equation models failed to confirm intermediate responses postulated to mediate the priming effect, including responses postulated to be mediated by stoichiometry and microbial activation. Specifically, priming was not clearly associated with changes in microbial biomass or turnover, nor with extracellular enzyme activities or the microbial C-to-N ratio. The strongest explanatory pathways in the structural equation models were the substrate, soil, and C-to-N ratio treatments themselves, with no intermediates, suggesting that either these measurements lacked sufficient sensitivity to reveal causal relationships, or the actual drivers for priming were not included in the ancillary measurements. While we observed consistent changes in priming caused by the amount and C-to-N ratio of the added substrate across a wide array of soils, our findings did not clearly conform to common models offered for the priming effect. Because priming is a residual flux involving diverse substrates of varying chemical composition, a simple and generalizable explanation of the phenomenon may be elusive.