Use and misuse of PLFA measurements in soils
TL;DR: In this article, the authors discuss problems in PLFA interpretation, the extent of turnover of PLFAs in soil, and the flawed use of diversity indices to evaluate PLFA patterns.
Abstract: The determination of the phospholipid fatty acid (PLFA) pattern of soil organisms has become one of the most commonly used methods to study microbial community structure. Here we recapitulate the background of our work applying the PLFA method to soil in the early 1990s. We also stress that although the PLFA method was, and still is, a rapid and sensitive method to detect changes in the microbial community in soil, as with all popular methods it can be misused. We discuss problems in PLFA interpretation, the extent of turn-over of PLFAs in soil, and the flawed use of diversity indices to evaluate PLFA patterns.
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TL;DR: The remediation of heavy metal(loid) contaminated soils through manipulating their bioavailability using a range of soil amendments will be presented.
1,507 citations
Swedish University of Agricultural Sciences1, Uppsala University2, University of Tartu3, Max Delbrück Center for Molecular Medicine4, Charité5, Leiden University6, University of Wisconsin-Madison7, Braunschweig University of Technology8, Technical University of Madrid9, Wageningen University and Research Centre10, University of California, Riverside11, University of Oslo12, Lund University13, ETH Zurich14, American Museum of Natural History15, University of Würzburg16
TL;DR: It is shown that bacterial, but not fungal, genetic diversity is highest in temperate habitats and that microbial gene composition varies more strongly with environmental variables than with geographic distance, and that the relative contributions of these microorganisms to global nutrient cycling varies spatially.
Abstract: Soils harbour some of the most diverse microbiomes on Earth and are essential for both nutrient cycling and carbon storage. To understand soil functioning, it is necessary to model the global distribution patterns and functional gene repertoires of soil microorganisms, as well as the biotic and environmental associations between the diversity and structure of both bacterial and fungal soil communities1–4. Here we show, by leveraging metagenomics and metabarcoding of global topsoil samples (189 sites, 7,560 subsamples), that bacterial, but not fungal, genetic diversity is highest in temperate habitats and that microbial gene composition varies more strongly with environmental variables than with geographic distance. We demonstrate that fungi and bacteria show global niche differentiation that is associated with contrasting diversity responses to precipitation and soil pH. Furthermore, we provide evidence for strong bacterial–fungal antagonism, inferred from antibiotic-resistance genes, in topsoil and ocean habitats, indicating the substantial role of biotic interactions in shaping microbial communities. Our results suggest that both competition and environmental filtering affect the abundance, composition and encoded gene functions of bacterial and fungal communities, indicating that the relative contributions of these microorganisms to global nutrient cycling varies spatially.
1,108 citations
TL;DR: The results presented in this review show that antibiotics affect soil microorganisms by changing their enzyme activity and ability to metabolize different carbon sources, as well as by altering the overall microbial biomass and the relative abundance of different groups in microbial communities.
Abstract: Antibiotics play a key role in the management of infectious diseases in humans, animals, livestock, and aquacultures all over the world. The release of increasing amount of antibiotics into waters and soils creates a potential threat to all microorganisms in these environments. This review addresses issues related to the fate and degradation of antibiotics in soils and the impact of antibiotics on the structural, genetic and functional diversity of microbial communities. Due to the emergence of bacterial resistance to antibiotics, which is considered a worldwide public health problem, the abundance and diversity of antibiotic resistance genes (ARGs) in soils are also discussed. When antibiotic residues enter the soil, the main processes determining their persistence are sorption to organic particles and degradation/transformation. The wide range of DT50 values for antibiotic residues in soils shows that the processes governing persistence depend on a number of different factors, e.g., physico-chemical properties of the residue, characteristics of the soil, and climatic factors (temperature, rainfall, and humidity). The results presented in this review show that antibiotics affect soil microorganisms by changing their enzyme activity and ability to metabolize different carbon sources, as well as by altering the overall microbial biomass and the relative abundance of different groups (i.e., Gram-negative bacteria, Gram-positive bacteria, and fungi) in microbial communities. Studies using methods based on analyses of nucleic acids prove that antibiotics alter the biodiversity of microbial communities and the presence of many types of ARGs in soil are affected by agricultural and human activities. It is worth emphasizing that studies on ARGs in soil have resulted in the discovery of new genes and enzymes responsible for bacterial resistance to antibiotics. However, many ambiguous results indicate that precise estimation of the impact of antibiotics on the activity and diversity of soil microbial communities is a great challenge.
426 citations
TL;DR: It is found that the agricultural and early successional land uses harbored unique soil bacterial communities that exhibited distinct temporal patterns that were likely a product of complex interactions between the soil environment and the more diverse plant community.
Abstract: Although numerous studies have investigated changes in soil microbial communities across space, questions about the temporal variability in these communities and how this variability compares across soils have received far less attention. We collected soils on a monthly basis (May to November) from replicated plots representing three land-use types (conventional and reduced-input row crop agricultural plots and early successional grasslands) maintained at a research site in Michigan, USA. Using barcoded pyrosequencing of the 16S rRNA gene, we found that the agricultural and early successional land uses harbored unique soil bacterial communities that exhibited distinct temporal patterns. α-Diversity, the numbers of taxa or lineages, was significantly influenced by the sampling month with the temporal variability in α-diversity exceeding the variability between land-use types. In contrast, differences in community composition across land-use types were reasonably constant across the 7-month period, suggesting that the time of sampling is less important when assessing β-diversity patterns. Communities in the agricultural soils were most variable over time and the changes were significantly correlated with soil moisture and temperature. Temporal shifts in bacterial community composition within the successional grassland plots were less predictable and are likely a product of complex interactions between the soil environment and the more diverse plant community. Temporal variability needs to be carefully assessed when comparing microbial diversity across soil types and the temporal patterns in microbial community structure can not necessarily be generalized across land uses, even if those soils are exposed to the same climatic conditions.
402 citations
Cites methods from "Use and misuse of PLFA measurements..."
...Clearly our ability to resolve temporal variability in soil microbial communities will depend on the analytical methods employed and the sampling design (Frostegard et al., 2011), with some DNA-based studies indicating that spatial variability may exceed temporal variability across broader geographic gradients (Fierer and Jackson, 2006; Griffiths et al....
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...…our ability to resolve temporal variability in soil microbial communities will depend on the analytical methods employed and the sampling design (Frostegard et al., 2011), with some DNA-based studies indicating that spatial variability may exceed temporal variability across broader geographic…...
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TL;DR: A critical review and synthesis of the most commonly applied “open-format" and “closed-format” detection technologies for interrogating microbial communities and discusses their characteristics, advantages, and disadvantages within the context of environmental applications.
Abstract: Understanding the structure, functions, activities and dynamics of microbial communities in natural environments is one of the grand challenges of 21st century science. To address this challenge, over the past decade, numerous technologies have been developed for interrogating microbial communities, of which some are amenable to exploratory work (e.g., high- throughput sequencing and phenotypic screening) and others depend on reference genes or genomes (e.g., phylogenetic and functional gene arrays). Here, we provide a critical review and synthesis of the most commonly applied "open-format" and "closed-format" detection technologies. We discuss their characteristics, advantages, and disadvantages within the context of environmental applications and focus on analysis of complex microbial systems, such as those in soils, in which diversity is high and reference genomes are few. In addition, we discuss crucial issues and considerations associated with applying complemen- tary high-throughput molecular technologies to address important ecological questions.
362 citations
Cites background from "Use and misuse of PLFA measurements..."
...Since 1990, various molecular methods capable of tracking one to hundreds of biomarkers have been widely used to analyze microbial community structure, such as PCR amplification-based gene cloning, sequencing of 16S rRNA genes (21) and functional genes (22), amplified ribosomal DNA restriction analysis (23), denaturing gradient gel electrophoresis (24), terminal restriction fragment length polymorphism (25), phospholipid fatty acid analysis (26), and BioLog EcoPlates for measuring carbon and nitrogen metabolisms (27)....
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References
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TL;DR: The lipid decomposition studies in frozen fish have led to the development of a simple and rapid method for the extraction and purification of lipids from biological materials that has been applied to fish muscle and may easily be adapted to use with other tissues.
Abstract: Lipid decomposition studies in frozen fish have led to the development of a simple and rapid method for the extraction and purification of lipids from biological materials. The entire procedure can...
46,099 citations
"Use and misuse of PLFA measurements..." refers methods in this paper
...Although our method was based primarily on the Bligh & Dyer extraction technique (Bligh and Dyer, 1959), with the modifications used in David White’s laboratory, we also introduced some of our own modifications, e.g. the use of citrate buffer instead of phosphate buffer....
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...Although our method was based primarily on the Bligh & Dyer extraction technique (Bligh and Dyer, 1959), with the modifications used in David White’s laboratory, we also introduced some of our own modifications, e....
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TL;DR: The results suggest that the structure of soil bacterial communities is predictable, to some degree, across larger spatial scales, and the effect of soil pH on bacterial community composition is evident at even relatively coarse levels of taxonomic resolution.
Abstract: Soils harbor enormously diverse bacterial populations, and soil bacterial communities can vary greatly in composition across space. However, our understanding of the specific changes in soil bacterial community structure that occur across larger spatial scales is limited because most previous work has focused on either surveying a relatively small number of soils in detail or analyzing a larger number of soils with techniques that provide little detail about the phylogenetic structure of the bacterial communities. Here we used a bar-coded pyrosequencing technique to characterize bacterial communities in 88 soils from across North and South America, obtaining an average of 1,501 sequences per soil. We found that overall bacterial community composition, as measured by pairwise UniFrac distances, was significantly correlated with differences in soil pH (r = 0.79), largely driven by changes in the relative abundances of Acidobacteria, Actinobacteria, and Bacteroidetes across the range of soil pHs. In addition, soil pH explains a significant portion of the variability associated with observed changes in the phylogenetic structure within each dominant lineage. The overall phylogenetic diversity of the bacterial communities was also correlated with soil pH (R2 = 0.50), with peak diversity in soils with near-neutral pHs. Together, these results suggest that the structure of soil bacterial communities is predictable, to some degree, across larger spatial scales, and the effect of soil pH on bacterial community composition is evident at even relatively coarse levels of taxonomic resolution.
3,151 citations
"Use and misuse of PLFA measurements..." refers background in this paper
...The canonical importance of pH in determining microbial community composition in soil has recently been re-emphasized using molecular techniques (Lauber et al., 2009; Rousk et al., 2010a)....
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TL;DR: Soils collected across a long-term liming experiment were used to investigate the direct influence of pH on the abundance and composition of the two major soil microbial taxa, fungi and bacteria, and both the relative abundance and diversity of bacteria were positively related to pH.
Abstract: Soils collected across a long-term liming experiment (pH 4.0-8.3), in which variation in factors other than pH have been minimized, were used to investigate the direct influence of pH on the abundance and composition of the two major soil microbial taxa, fungi and bacteria. We hypothesized that bacterial communities would be more strongly influenced by pH than fungal communities. To determine the relative abundance of bacteria and fungi, we used quantitative PCR (qPCR), and to analyze the composition and diversity of the bacterial and fungal communities, we used a bar-coded pyrosequencing technique. Both the relative abundance and diversity of bacteria were positively related to pH, the latter nearly doubling between pH 4 and 8. In contrast, the relative abundance of fungi was unaffected by pH and fungal diversity was only weakly related with pH. The composition of the bacterial communities was closely defined by soil pH; there was as much variability in bacterial community composition across the 180-m distance of this liming experiment as across soils collected from a wide range of biomes in North and South America, emphasizing the dominance of pH in structuring bacterial communities. The apparent direct influence of pH on bacterial community composition is probably due to the narrow pH ranges for optimal growth of bacteria. Fungal community composition was less strongly affected by pH, which is consistent with pure culture studies, demonstrating that fungi generally exhibit wider pH ranges for optimal growth.
2,966 citations
"Use and misuse of PLFA measurements..." refers background in this paper
...…to pH reported in our 1993 paper (e.g. an increase in the abundance of 16:1u5 and some other mono-unsaturated PLFAs, and a decrease in cy19:0, with increasing pH), have been found in many other soils and were recently suggested to be general indicators of direct pH effects (Rousk et al., 2010b)....
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...The canonical importance of pH in determining microbial community composition in soil has recently been re-emphasized using molecular techniques (Lauber et al., 2009; Rousk et al., 2010a)....
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TL;DR: The cell content of 12 bacterial phospholipid fatty acids (PLFA) was determined in bacteria extracted from soil by homogenization/centrifugation and the soil content of the PLFA 18:2ω6 was correlated with the ergosterol content, which supports the use of this PLFA as an indicator of fungal biomass.
Abstract: The cell content of 12 bacterial phospholipid fatty acids (PLFA) was determined in bacteria extracted from soil by homogenization/centrifugation. The bacteria were enumerated using acridine orange direct counts. An average of 1.40×10-17 mol bacterial PLFA cell-1 was found in bacteria extracted from 15 soils covering a wide range of pH and organic matter contents. With this factor, the bacterial biomass based on PLFA analyses of whole soil samples was calculated as 1.0–4.8 mg bacterial C g-1 soil C. The corresponding range based on microscopical counts was 0.3–3.0 mg bacterial C g-1 soil C. The recovery of bacteria from the soils using homogenization/centrifugation was 2.6–16% (mean 8.7%) measured by PLFA analysis, and 12–61% (mean 26%) measured as microscopical counts. The soil content of the PLFA 18:2ω6 was correlated with the ergosterol content (r=0.92), which supports the use of this PLFA as an indicator of fungal biomass. The ratio 18:2ω6 to bacterial PLFA is therefore suggested as an index of the fungal:bacterial biomass ratio in soil. An advantage with the method based on PLFA analyses is that the same technique and even the same sample is used to determine both fungi and bacteria. The fungal:bacterial biomass ratio calculated in this way was positively correlated with the organic matter content of the soils (r=0.94).
2,256 citations
"Use and misuse of PLFA measurements..." refers background or methods in this paper
...The relative abundance of fungi and bacteria, often referred as the fungal/bacterial ratio, can be calculated from the amounts of PLFAs specific to these respective groups (Frostegård and Bååth, 1996) and has been used widely for comparing soils and treatments....
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...The conversion factors established to estimate fungal and bacterial biomass-C from amounts of PLFA show good correlation with other ways of determining the biomass of these groups (Klamer and Bååth, 2004; Frostegård and Bååth, 1996) and give reliable determinationsof the amounts of different carbon substrates incorporated into soil bacterial biomass (Jia et al....
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...…bacterial biomass-C from amounts of PLFA show good correlation with other ways of determining the biomass of these groups (Klamer and Bååth, 2004; Frostegård and Bååth, 1996) and give reliable determinationsof the amounts of different carbon substrates incorporated into soil bacterial biomass…...
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