Plot-scale manipulations of organic matter inputs to soils correlate with shifts in microbial community composition in a lowland tropical rain forest

Nemergut, Diana R.; Cleveland, Cory C.; Wieder, William R.; Washenberger, Christopher L.; Townsend, Alan R.

doi:10.1016/j.soilbio.2010.08.011

Cited by 223 publications

(126 citation statements)

References 36 publications

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“…As microbial community structure drives function, some argue that there is value in knowing 'who does what' to understand and predict ecosystem processes (Zak et al, 2003;Monson et al, 2006;Van Der Heijden et al, 2008). However, as mentioned above, many studies reveal that environmental factors are important determinants of microbial community structure (Fierer and Jackson, 2006;Lozupone and Knight, 2007;Logue and Lindstrom, 2010;Nemergut et al, 2010). Also, these same parameters are vital in regulating ecosystem processes (Bonan and Shugart 1989;Paul and Clark, 1996), raising the question: how much added value is provided by detailed investigations of microbial structure data?…”

Section: Discussionmentioning

confidence: 99%

“…DNA extraction and pyrosequencing of partial 16 S rRNA genes DNA was isolated using the MO BIO Power Soil DNA Extraction kit (MO BIO Laboratories, Carlsbad, CA, USA), and was processed as described in Nemergut et al, (2010) and Knelman et al, (2012). A fragment of the 16S rRNA gene encoding the V1-V2 region was amplified using modified primers of 27F and 338R adapted for Titanium chemistry (454 Life Sciences, Bradford, CT, USA).…”

Section: Methodsmentioning

confidence: 99%

“…For example, ample evidence suggests that different ecosystems host distinct types of microbes (Lozupone and Knight, 2007;Nemergut et al, 2011), and that these community differences likely reflect selection (sensu Vellend, 2010) acting on trait differences between suites of organisms. Indeed, evidence supports the role of environmental parameters, including pH, salinity and the abundance and quality of carbon (C) in structuring microbial communities (Fierer and Jackson, 2006;Lozupone and Knight, 2007;Logue and Lindströ m, 2010;Nemergut et al, 2010). Community assembly processes driven by environmental parameters acting on traits are often called 'niche-based' (the term we use here) but they have also been referred to as 'habitat filters' and 'deterministic processes' in the literature.…”

Section: Introductionmentioning

confidence: 94%

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Changes in assembly processes in soil bacterial communities following a wildfire disturbance

et al. 2013

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Although recent work has shown that both deterministic and stochastic processes are important in structuring microbial communities, the factors that affect the relative contributions of niche and neutral processes are poorly understood. The macrobiological literature indicates that ecological disturbances can influence assembly processes. Thus, we sampled bacterial communities at 4 and 16 weeks following a wildfire and used null deviation analysis to examine the role that time since disturbance has in community assembly. Fire dramatically altered bacterial community structure and diversity as well as soil chemistry for both time-points. Community structure shifted between 4 and 16 weeks for both burned and unburned communities. Community assembly in burned sites 4 weeks after fire was significantly more stochastic than in unburned sites. After 16 weeks, however, burned communities were significantly less stochastic than unburned communities. Thus, we propose a three-phase model featuring shifts in the relative importance of niche and neutral processes as a function of time since disturbance. Because neutral processes are characterized by a decoupling between environmental parameters and community structure, we hypothesize that a better understanding of community assembly may be important in determining where and when detailed studies of community composition are valuable for predicting ecosystem function.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 94%

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Changes in assembly processes in soil bacterial communities following a wildfire disturbance

et al. 2013

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“…As the amendment time increases, easily degradable component (e.g., low molecular carbohydrates, cellulose, and hemicellulose) of stubble is generally consumed by some copiotrophs, and the remainder (e.g., lignin and polyphenols) is recalcitrant and mainly degraded by oligotrophs. Previous reports have described that copiotrophic bacteria (e.g., Alpha-, Beta-, Gammaproteobacteria, and Bacteroidetes) thrived under conditions where substrate availability was high (Fierer et al, 2007;Eilers et al, 2010;Nemergut et al, 2010), whereas oligotrophic bacteria (e.g., Deltaproteobacteria and Acidobacteria) were more abundant under nutrient-limited conditions (Bernard et al, 2007;Bastian et al, 2009;Pascault et al, 2013). The significant decrease in the relative abundance of Burkholderiales (belonging to Betaproteobacteria) at days 80 and 200 compared to day 20 of the incubation period, and the consistent decrease in the relative abundance of Sphingobacteriales (belonging to Bacteroidetes) with increasing amendment time further confirms the copiotrophic/oligotrophic model.…”

Section: Discussionmentioning

confidence: 99%

Bacterial community structure in maize stubble-amended soils with different moisture levels estimated by bar-coded pyrosequencing

Lin

Zhang

Zhao

et al. 2015

Applied Soil Ecology

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It is of ecological significance to investigate microbial communities in response to straw amendment and moisture in arable soils. However, in Chinese fluvo-aquic soils, these responses are still poorly understood. We designed an incubation experiment involving two soils with and without the addition of maize stubble at two moisture levels, and bacterial community structure at days 20, 80, and 200 after the start of incubation was assessed via bar-coded pyrosequencing of the 16S rDNA amplicons. In the presence of stubble with identical moisture level, we observed higher bacterial diversity and richness in long-term organic manure-fertilized soil compared with the unfertilized soil at days 20 and 80, which we attributed to the different quality and quantity of organic matter between the two soils. However, there was no significant difference in bacterial diversity and richness between the two soils at day 200, indicating that long-term straw amendment probably lessens the difference in bacterial community structure between the two soils. In the amended soils bacterial diversity, richness, and community composition at 25% of the water-holding capacity distinctly differed from those at 55% of the waterholding capacity, indicating that moisture strongly affects bacterial distribution in the amended soils. As stubble-C availability declined over time, the dominance of copiotrophic population weakened, and oligotrophic population was moderately abundant. Finally, our study suggests that dissolved organic carbon, which drives redistribution in copiotrophic and oligotrophic categories in response to the varying water and stubble-C availability, is a determinant of bacterial community composition in the amended soils.

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“…Different habitat types (e.g., seawater versus soils) harbor different suites of microorganisms (89), and a copious amount of data supports the role of a variety of environmental factors in determining bacterial assemblage structure and diversity, including pH, salinity, and the abundance and quality of carbon (59,88,90,91). Together, these relationships support the importance of selection via abiotic factors in determining microbial community structure.…”

Section: Selectionmentioning

confidence: 95%

Patterns and Processes of Microbial Community Assembly

Nemergut

Schmidt

Fukami

et al. 2013

Microbiol Mol Biol Rev

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1,325

1,177

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SUMMARY Recent research has expanded our understanding of microbial community assembly. However, the field of community ecology is inaccessible to many microbial ecologists because of inconsistent and often confusing terminology as well as unnecessarily polarizing debates. Thus, we review recent literature on microbial community assembly, using the framework of Vellend (Q. Rev. Biol. 85 :183–206, 2010) in an effort to synthesize and unify these contributions. We begin by discussing patterns in microbial biogeography and then describe four basic processes (diversification, dispersal, selection, and drift) that contribute to community assembly. We also discuss different combinations of these processes and where and when they may be most important for shaping microbial communities. The spatial and temporal scales of microbial community assembly are also discussed in relation to assembly processes. Throughout this review paper, we highlight differences between microbes and macroorganisms and generate hypotheses describing how these differences may be important for community assembly. We end by discussing the implications of microbial assembly processes for ecosystem function and biodiversity.

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Plot-scale manipulations of organic matter inputs to soils correlate with shifts in microbial community composition in a lowland tropical rain forest

Cited by 223 publications

References 36 publications

Changes in assembly processes in soil bacterial communities following a wildfire disturbance

Changes in assembly processes in soil bacterial communities following a wildfire disturbance

Bacterial community structure in maize stubble-amended soils with different moisture levels estimated by bar-coded pyrosequencing

Patterns and Processes of Microbial Community Assembly

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