Microbial decomposers not constrained by climate history along a Mediterranean climate gradient in southern California

Baker, Nameer; Khalili, Banafshe; Martiny, Jennifer B. H.; Allison, Steven D.

doi:10.1002/ecy.2345

Cited by 18 publications

(16 citation statements)

References 53 publications

(106 reference statements)

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“…S3). Bacterial biomass dominated in both the in situ leaf litter and in the transplanted litterbags, with fungal:bacterial ratios, estimated as grams carbon per gram dry leaf litter converted from bacterial flow cytometry counts and fungal hyphal abundance counts, ranging from 0.15 to 0.72 across the sites (SI Appendix, Table S2), similar to previous measurements (22).…”

Section: Resultssupporting

confidence: 74%

“…Moving the communities from colder, wetter sites at higher elevations to hotter, drier sites at lower elevations mimics the expected shift with climate change to more arid conditions in the southwest United States (20). While elevation gradients have long been used as "space for time" substitutions to predict how plant and animal communities will respond to climate change (21), the approach has only recently been applied to microbial communities (22,23).…”

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confidence: 99%

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Decomposition responses to climate depend on microbial community composition

Glassman

Weihe

et al. 2018

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

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Bacteria and fungi drive decomposition, a fundamental process in the carbon cycle, yet the importance of microbial community composition for decomposition remains elusive. Here, we used an 18-month reciprocal transplant experiment along a climate gradient in Southern California to disentangle the effects of the microbial community versus the environment on decomposition. Specifically, we tested whether the decomposition response to climate change depends on the microbial community. We inoculated microbial decomposers from each site onto a common, irradiated leaf litter within "microbial cages" that prevent microbial exchange with the environment. We characterized fungal and bacterial composition and abundance over time and investigated the functional consequences through litter mass loss and chemistry. After 12 months, microbial communities altered both decomposition rate and litter chemistry. Further, the functional measurements depended on an interaction between the community and its climate in a manner not predicted by current theory. Moreover, microbial ecologists have traditionally considered fungi to be the primary agents of decomposition and for bacteria to play a minor role. Our results indicate that not only does climate change and transplantation have differential legacy effects among bacteria and fungi, but also that bacterial communities might be less functionally redundant than fungi with regards to decomposition. Thus, it may be time to reevaluate both the role of microbial community composition in its decomposition response to climate and the relative roles of bacterial and fungal communities in decomposition.leaf litter decomposition | reciprocal transplant | bacteria | fungi | elevation gradient

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Section: Resultssupporting

confidence: 74%

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confidence: 99%

Decomposition responses to climate depend on microbial community composition

Glassman

Weihe

et al. 2018

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

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253

200

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“…We also detected higher bacterial abundance in litter than in surface bulk soil. We speculate that this pattern could be due to the larger amount and quality of organic matter in the litter, which provides more available substrates for the microbial activities (5, 15, 25). In addition, the smaller amount of clay particles might allow greater efficiency of cell extraction, which we did not test here.…”

Section: Discussionmentioning

confidence: 96%

“…Thus, both traditional microscopy and FCM require maximizing the extraction of cells from the matrix while minimizing cell damage. Various approaches involve the same two steps: (i) detachment of cells from soil particles (by shaking or sonication in a solution) and (ii) separation of the cells from soil debris (by filtration or centrifugation) before quantification (5, 6, 15). One promising method for the latter step is high-speed centrifugation of soil in a density gradient medium (4, 8, 9).…”

Section: Introductionmentioning

confidence: 99%

Optimization of a Method To Quantify Soil Bacterial Abundance by Flow Cytometry

Khalili

Weihe

Kimball

et al. 2019

mSphere

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Bacterial abundance is a fundamental metric for understanding the population dynamics of soil bacteria and their role in biogeochemical cycles. Despite its importance, methodological constraints hamper our ability to assess bacterial abundance in terrestrial environments. Here, we aimed to optimize the use of flow cytometry (FCM) to assay bacterial abundances in soil while providing a rigorous quantification of its limitations. Soil samples were spiked with Escherichia coli to evaluate the levels of recovery efficiency among three extraction approaches. The optimized method added a surfactant (a tetrasodium pyrophosphate [TSP] buffer) to 0.1 g of soil, applied an intermediate degree of agitation through shaking, and used a Nycodenz density gradient to separate the cells from background debris. This procedure resulted in a high (average, 89%) level of cell recovery. Recovery efficiencies did not differ significantly among sites across an elevation gradient but were positively correlated with percent carbon in the soil samples. Estimated abundances were also highly repeatable between technical replicates. The method was applied to samples from two field studies and, in both cases, was sensitive enough to detect treatment and site differences in bacterial abundances. We conclude that FCM offers a fast and sensitive method to assay soil bacterial abundance from relatively small amounts of soil. Further work is needed to assay differential biases of the method across a wider range of soil types. IMPORTANCE The ability to quantify bacterial abundance is important for understanding the contributions of microbial communities in soils, but such assays remain difficult and time-consuming. Flow cytometry offers a fast and direct way to count bacterial cells, but several concerns remain in applying the technique to soils. This study aimed to improve the efficiency of the method for soil while quantifying its limitations. We demonstrated that an optimized procedure was sensitive enough to capture differences in bacterial abundances among treatments and ecosystems in two field studies.

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“…Root-associated microbial communities are important mediators of plant traits and soil 41 processes. For example, microorganisms can accelerate nutrient cycling and increase nutrient 42 availability to plants (Baker et al 2018). Some microbes fix nitrogen (Boyd and Peters 2013;43 Mus et al 2016) and provide plants with nutrients (Shakeel et al 2015), with effects that scale to 44 influence global nutrient cycles (Finzi et al 2015).…”

Section: Introduction 40mentioning

confidence: 99%

Plant species and soil type influence rhizosphere bacterial composition and seedling establishment on serpentine soils

2018

Preprint

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10Root-associated microbial communities influence plant phenotype, growth and local abundance, 11 yet the factors that structure these microbial communities are still poorly understood. California 12 landscapes contain serpentine soils, which are nutrient-poor and high in heavy metals, and 13 distinct from neighboring soils. Here, we surveyed the rhizoplane of serpentine-indifferent plants 14 species growing on serpentine and non-serpentine soils to determine the relative influence of 15 plant identity and soil chemistry on rhizoplane microbial community structure using 16S rRNA 16 metabarcoding. Additionally, we experimentally examined if locally adapted microorganisms 17 enhance plant growth in serpentine soil. Plant species, soil chemistry, and the interaction 18 between them were important in structuring rhizoplane bacterial communities in both the field 19 and experimental soils. In the experiment, rhizoplane microbial community source influenced 20 seedling survival, but plant growth phenotypes measured were largely invariant to microbial 21 community with a few exceptions. Results from the field sampling suggest that plant species 22 associate with specific microbial communities even across chemically distinct soils, and that 23 microbial communities can differentially influence seedling survival on harsh serpentine soils. 24 Words: 169 25Importance 26Microbial communities on plant roots can influence host plant phenotype, survival, and fitness, 27 with community and ecosystem consequences. However, which factors structure microbial 28 community structure is poorly understood, particularly across large gradients in soil properties. 29The survey and experiment described here shows that plant species host distinct microbiomes 30 despite strong turnover in soil chemistry, although soil type also influences bacterial structure. 31These results suggest that host specificity and soil conditions are both strong drivers of 32 rhizoplane bacterial composition in serpentine ecosystems and influence plant seedling 33 establishment. These results imply that plant species can recruit relatively convergent 34 microbiomes from distinct microbial communities found on different soil types and that soil 35 microbial communities influence seedling establishment. 36 37 38 39 Plant collection 131Plantago erecta, T. fucatum, C. sparsiflora and G. tricolor were collected from two geographically 132

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Microbial decomposers not constrained by climate history along a Mediterranean climate gradient in southern California

Cited by 18 publications

References 53 publications

Decomposition responses to climate depend on microbial community composition

Decomposition responses to climate depend on microbial community composition

Optimization of a Method To Quantify Soil Bacterial Abundance by Flow Cytometry

Plant species and soil type influence rhizosphere bacterial composition and seedling establishment on serpentine soils

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