Diversity and dynamics of microbial communities in soils from agro‐ecosystems

Buckley, Daniel H.; Schmidt, Thomas M.

doi:10.1046/j.1462-2920.2003.00404.x

Cited by 271 publications

(175 citation statements)

References 63 publications

(81 reference statements)

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“…Our finding that management history had a stronger impact than substrate addition on microbial community diversity and structure is consistent with other studies, which found that management had a long lasting legacy effect on microbial community structure [8,11,13,14]. Bacteria in organically managed soils had a large number of TRFs (one-third of all TRFs) that were unique to that soil community, while all TRFs present in conventionally managed soils were shared with organically managed soils (Fig.…”

Section: Discussionsupporting

confidence: 91%

“…Organic management practices using diverse rotations and additions of organic residues affect microbial community structure over the long term through buildup of soil organic matter (SOM) and changes in SOM chemistry [6,7,[12][13][14]. In addition, greater crop diversity alters plant litter inputs and can presumably increase the number of ecological niches available for soil microbes [7,11].…”

Section: Introductionmentioning

confidence: 99%

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Agricultural Management and Labile Carbon Additions Affect Soil Microbial Community Structure and Interact with Carbon and Nitrogen Cycling

2013

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We investigated how conversion from conventional agriculture to organic management affected the structure and biogeochemical function of soil microbial communities. We hypothesized the following. (1) Changing agricultural management practices will alter soil microbial community structure driven by increasing microbial diversity in organic management. (2) Organically managed soil microbial communities will mineralize more N and will also mineralize more N in response to substrate addition than conventionally managed soil communities. (3) Microbial communities under organic management will be more efficient and respire less added C. Soils from organically and conventionally managed agroecosystems were incubated with and without glucose ( 13 C) additions at constant soil moisture. We extracted soil genomic DNA before and after incubation for TRFLP community fingerprinting of soil bacteria and fungi. We measured soil C and N pools before and after incubation, and we tracked total C respired and N mineralized at several points during the incubation. Twenty years of organic management altered soil bacterial and fungal community structure compared to continuous conventional management with the bacterial differences caused primarily by a large increase in diversity. Organically managed soils mineralized twice as much NO3 − as conventionally managed ones (44 vs. 23 μg N/g soil, respectively) and increased mineralization when labile C was added. There was no difference in respiration, but organically managed soils had larger pools of C suggesting greater efficiency in terms of respiration per unit soil C. These results indicate that the organic management induced a change in community composition resulting in a more diverse community with enhanced activity towards labile substrates and greater capacity to mineralize N.2

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Section: Discussionsupporting

confidence: 91%

Section: Introductionmentioning

confidence: 99%

Agricultural Management and Labile Carbon Additions Affect Soil Microbial Community Structure and Interact with Carbon and Nitrogen Cycling

2013

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“…However, rDNA-based techniques only identify populations that are potentially active. Because growing cells require ribosomes for protein synthesis, ribosomal RNA (rRNA) can be used to characterize the active portion of communities (27). The simultaneous characterization of microbial communities by rRNA and rDNA fingerprinting is analogous to surveys of plant communities and their associated seed banks (28).…”

Section: Resultsmentioning

confidence: 99%

Dormancy contributes to the maintenance of microbial diversity

Jones

Lennon

2010

Proc. Natl. Acad. Sci. U.S.A.

753

650

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Dormancy is a bet-hedging strategy used by a variety of organisms to overcome unfavorable environmental conditions. By entering a reversible state of low metabolic activity, dormant individuals become members of a seed bank, which can determine community dynamics in future generations. Although microbiologists have documented dormancy in both clinical and natural settings, the importance of seed banks for the diversity and functioning of microbial communities remains untested. Here, we develop a theoretical model demonstrating that microbial communities are structured by environmental cues that trigger dormancy. A molecular survey of lake ecosystems revealed that dormancy plays a more important role in shaping bacterial communities than eukaryotic microbial communities. The proportion of dormant bacteria was relatively low in productive ecosystems but accounted for up to 40% of taxon richness in nutrient-poor systems. Our simulations and empirical data suggest that regional environmental cues and dormancy synchronize the composition of active communities across the landscape while decoupling active microbes from the total community at local scales. Furthermore, we observed that rare bacterial taxa were disproportionately active relative to common bacterial taxa, suggesting that microbial rank-abundance curves are more dynamic than previously considered. We propose that repeated transitions to and from the seed bank may help maintain the high levels of microbial biodiversity that are observed in nearly all ecosystems.biodiversity | ecosystem function | microbial ecology | modeling | seed bank

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“…In this sense, our results are consistent with studies in nontropical areas, in which the structure of microbial communities in the soil over two years in a series of replicated plots was investigated. The studied area included cultivated fields, fields abandoned from cultivation and fields with no history of cultivation, in sites established in 1989 to study ecological processes in agro-ecosystems in the state of Michigan [38]. These authors showed that fields with no history of cultivation differed significantly from cultivated fields.…”

Section: Model I Of Amazonian Agricultural System: the "Slash-and-burmentioning

confidence: 99%

A Molecular Survey of the Diversity of Microbial Communities in Different Amazonian Agricultural Model Systems

et al. 2010

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Abstract:The processes of land conversion and agricultural intensification are a significant cause of biodiversity loss, with consequent negative effects both on the environment and the sustainability of food production. The anthrosols associated with pre-Colombian settlements in the Amazonian region are examples of how anthropogenic activities may sustain the native populations against harsh tropical environments for human establishment, even without a previous intentionality of anthropic soil formation. In a case study (Model I-"Slash-andBurn") the community structures detected by automated ribosomal intergenic spacer analysis (ARISA) revealed that soil archaeal, bacterial and fungal communities are heterogeneous and each capable of responding differently to environmental characteristics. ARISA data evidenced considerable difference in structure existing between microbial communities in forest and agricultural soils. In a second study (Model II-"Anthropogenic Soil"), the bacterial community structures revealed by terminal restriction fragment length polymorphism (T-RFLP) differed among an Amazonian Dark Earth (ADE), black carbon (BC) and its adjacent non-anthropogenic oxisoil. The bacterial 16S rRNA gene (OTU) richness estimated by pyrosequencing was higher in ADE than BC. The most abundant bacterial phyla in ADE soils and BC were Proteobacteria-24% ADE, 15% BC; Acidobacteria-10% ADE, 21% BC; Actinobacteria-7% ADE, 12% BC; Verrucomicrobia, 8% ADE; 9% BC; Firmicutes-3% ADE, 8% BC. Overall, unclassified bacteria corresponded to 36% ADE, and 26% BC. Regardless of current land uses, our data suggest OPEN ACCESSDiversity 2010, 2 788 that soil microbial community structures may be strongly influenced by the historical soil management and that anthrosols in Amazonia, of anthropogenic origins, in addition to their capacity of enhancing crop yields, may also improve microbial diversity, with the support of the black carbon, which may sustain a particular and unique habitat for the microbes.

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Diversity and dynamics of microbial communities in soils from agro‐ecosystems

Cited by 271 publications

References 63 publications

Agricultural Management and Labile Carbon Additions Affect Soil Microbial Community Structure and Interact with Carbon and Nitrogen Cycling

Agricultural Management and Labile Carbon Additions Affect Soil Microbial Community Structure and Interact with Carbon and Nitrogen Cycling

Dormancy contributes to the maintenance of microbial diversity

A Molecular Survey of the Diversity of Microbial Communities in Different Amazonian Agricultural Model Systems

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