Biology subjects

Shade, A.

Publications and source records attributed to Shade, A..

6 recordsLinked to original sources

bioRxiv2018

Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops

Perennial grasses are promising feedstocks for biofuel production. The phyllosphere (aerial surfaces) of these cellulosic crops provide a sizable surface area of microbial habitation. Leaf microbial communities may benefit the host plant, have consequence for biomass deconstruction, and interact with foliar pathogens. Here, we characterized the origins, diversity, and assembly of bacterial and archaeal communities of two perennial cellulosic feedstocks: switchgrass (Panicum virgatum L.) and miscanthus (Miscanthus x giganteus). We used 16S rRNA gene sequencing to assess microbiome structure on leaves and soils, following crop phenology every three weeks from pre-emergence through senescence for one miscanthus growing season and two consecutive switchgrass seasons. We found abundant and persistent core leaf taxa that originated in soil but were adapted for life on the leaf, rather than vagabonds that randomly disperse from air or soil. Seasonal and host-specific assembly suggested a functional relationship between the phyllosphere microbiomes and plants. This foundational knowledge advances goals to leverage native microbiomes to promote crop wellness and productivity in the field, and specifically in support of biofuels agriculture.

microbiology↗

bioRxiv2018

Targeting microbial arsenic resistance genes: a new bioinformatic toolkit informs arsenic ecology and evolution in soil genomes and metagenomes

Environmental resistomes include transferable microbial genes. One important resistome component is resistance to arsenic, a ubiquitous and toxic metalloid that can have negative and chronic consequences for human and animal health. The distribution of arsenic resistance and metabolism genes in the environment is not well understood. However, microbial communities and their resistomes mediate key transformations of arsenic that are expected to impact both biogeochemistry and local toxicity. We examined the phylogenetic diversity, genomic location (chromosome or plasmid), and biogeography of arsenic resistance and metabolism genes in 922 soil genomes and 38 metagenomes. To do so, we developed a bioinformatic toolkit that includes BLAST databases, hidden Markov models and resources for gene-targeted assembly of nine arsenic resistance and metabolism genes: acr3, aioA, arsB, arsC (grx), arsC (trx), arsD, arsM, arrA, and arxA. Though arsenic related genes were common, they were not universally detected, contradicting the common conjecture that all organisms have them. From major clades of arsenic related genes, we inferred their potential for horizontal and vertical transfer. Different types and proportions of genes were detected across soils, suggesting microbial community composition will, in part, determine local arsenic toxicity and biogeochemistry. While arsenic related genes were globally distributed, particular sequence variants were highly endemic (e.g., acr3), suggesting dispersal limitation. The gene encoding arsenic methylase arsM was unexpectedly abundant in soil metagenomes (median 48%), suggesting that it plays a prominent role in global arsenic biogeochemistry. Our analysis advances understanding of arsenic resistance, metabolism, and biogeochemistry, and our approach provides a roadmap for the ecological investigation of environmental resistomes.

microbiology↗

bioRxiv2018

16S rRNA:rDNA ratios and cell activity staining reveal consistent patterns of soil microbial activity

Microbial activity plays a major role in the processes that support life on Earth. Nevertheless, across diverse ecosystems many microbes are in a state of dormancy, characterized by strongly reduced metabolic rates. Of the methods used to assess microbial activity-dormancy dynamics, 16S rRNA: rDNA amplicons (\"16S ratios\") and active cell staining with 5-cyano-2,3-ditolyl tetrazolium chloride (CTC) are two of the most common, yet each method has its own limitations. To better understand the applicability and potential complementarity of these two methods, we conducted two experiments investigating microbial activity in the rhizosphere. In the first experiment, we treated corn rhizosphere soil with common phytohormones to simulate plant-soil signaling during plant stress, and in the second experiment, we used bean exposed to drought or nutrient enrichment to more directly assess the impacts of plant stress on soil microbial activity. Overall, 16S ratios revealed numerous taxa with detectable RNA but no detectable DNA. However, overarching patterns in percent activity across treatments were unaffected by the method used to account for active taxa, or by the threshold 16S ratio used for taxa to be classified as active. 16S ratio distributions were highly similar across microbial phyla and were only weakly correlated with ribosomal operon number. Lastly, over relatively short time courses, 16S ratios are responsive earlier than CTC staining, a finding potentially related to the temporal sensitivity of activity changes detectable by the two methods. Our results suggest that 16S ratios and CTC staining provide robust and complementary estimates of bulk community activity.\n\nImportanceAlthough the majority of microorganisms in natural ecosystems are dormant, relatively little is known about the dynamics of the active and dormant microbial pools through both space and time. The limited knowledge of microbial activity-dormancy dynamics is in part due to uncertainty in the methods currently used to quantify active taxa. Here, we directly compared two of the most common methods (16S ratios and active cell staining) for estimating microbial activity in rhizosphere soil, and found that they were largely in agreement in the overarching patterns, suggesting that either method is robust for assessing comparative activity dynamics. Thus, our results suggest that 16S ratios and active cell staining provide robust and complementary information for measuring and interpreting microbial activity-dormancy dynamics in soils. They also support that 16S rRNA:rDNA ratios have comparative value and offer a high-throughput, sequencing-based option for understanding relative changes in microbiome activity.

microbiology↗

bioRxiv2018

RefSoil+: A reference for antimicrobial resistance genes on soil plasmids

Plasmids harbor transferable genes that contribute to the functional repertoire of microbial communities, yet their contributions to metagenomes are often overlooked. Environmental plasmids have the potential to spread antibiotic resistance to clinical microbial strains. In soils, high microbiome diversity and high variability in plasmid characteristics present a challenge for studying plasmids. To improve understanding of soil plasmids, we present RefSoil+, a database containing plasmid sequences from 922 soil microorganisms. Soil plasmids were relatively larger than other described plasmids, which is a trait associated with plasmid mobility. There was no relationship between chromosome size and plasmid size or number, suggesting that these genomic traits are independent in soil. Soil-associated plasmids, but not chromosomes, had fewer antibiotic resistance genes than other microorganisms. These data suggest that soils may offer limited opportunity for plasmid-mediated transfer of described antibiotic resistance genes. RefSoil+ can serve as a baseline for the diversity, composition, and host-associations of plasmid-borne functional genes in soil, a utility that will be enhanced as the database expands. Our study improves understanding of soil plasmids and provides a resource for assessing the dynamics of the genes that they carry, especially genes conferring antibiotic resistances.\n\nImportanceSoil-associated plasmids have the potential to transfer antibiotic resistance genes from environmental to clinical microbial strains, which is a public health concern. A specific resource is needed to aggregate knowledge of soil plasmid characteristics so that the content, host-associations, and dynamics of antibiotic resistance genes can be assessed and then tracked between the environment and the clinic. Here, we present RefSoil+, a database of soil-associated plasmids. RefSoil+ presents a contemporary snapshot of antibiotic resistance genes in soil that can serve as a reference as novel plasmids and transferred antibiotic resistances are discovered. Our study broadens our understanding of plasmids in soil and provides a community resource for investigating clinic-environment dynamics of important plasmid-associated genes, including antibiotic resistance genes.

microbiology↗

bioRxiv2018

Ecological selection for small microbial genomes along a temperate-to-thermal soil gradient

Small bacterial and archaeal genomes provide insights into the minimal requirements for life1 and seem to be widespread on the microbial phylogenetic tree2. We know that evolutionary processes, mainly selection and drift, can result in microbial genome reduction 3,4. However, we do not know the precise environmental pressures that constrain genome size in free-living microorganisms. A study including isolates 5 has shown that bacteria with high optimum growth temperatures, including thermophiles, often have small genomes 6. It is unclear how well this relationship may extend generally to microorganisms in nature 7,8, and in particular to those microbes inhabiting complex and highly variable environments like soil 3,6,9. To understand the genomic traits of thermally-adapted microorganisms, here we investigated bacterial and archaeal metagenomes from a 45{degrees}C gradient of temperate-to-thermal soils overlying the ongoing Centralia, Pennsylvania (USA) coal seam fire. There was a strong relationship between average genome size and temperature: hot soils had small genomes relative to ambient soils (Pearsons r = -0.910, p < 0.001). There was also an inverse relationship between soil temperature and cell size (Pearsons r = -0.65, p = 0.021), providing evidence that cell and genome size in the wild are together constrained by temperature. Notably, hot soils had different community structures than ambient soils, implicating ecological selection for thermo-tolerant cells that had small genomes, rather than contemporary genome streamlining within the local populations. Hot soils notably lacked genes for described two-component regulatory systems and antimicrobial production and resistance. Our work provides field evidence for the inverse relationship between microbial genome size and temperature requirements in a diverse, free-living community over a wide range of temperatures that support microbial life. Our findings demonstrate that ecological selection for thermophiles and thermo-tolerant microorganisms can result in smaller average genome sizes in situ, possibly because they have small genomes reminiscent of a more ancestral state.

microbiology↗

bioRxiv2017

Bacterial community composition and dynamics spanning five years in freshwater bog lakes

Bacteria play a key role in freshwater biogeochemical cycling, but long-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We used a multi-year time series of 16S rRNA gene amplicon sequencing data from eight bog lakes to census the freshwater bacterial community and observe annual and seasonal trends in abundance. Multiple sites and sampling events were necessary to begin to fully describe the bacterial communities. Each lake and layer contained a distinct bacterial community, with distinct levels of richness and indicator taxa that likely reflected the environmental conditions of each site. The community present in each year and site was also unique. Despite high interannual variability in community composition, we detected a core community of ubiquitous freshwater taxa. Although trends in abundance did not repeat annually, each freshwater lineage within the communities had a consistent lifestyle, defined by persistence, abundance, and variability. The results of our analysis emphasize the importance of long-term observations, as analyzing only a single year of data would not have allowed us to describe the dynamics and composition of these freshwater bacterial communities to the extent presented here.\n\nImportanceLakes are excellent systems for investigating bacterial community dynamics because they have clear boundaries and strong environmental gradients. The results of our research demonstrate that bacterial community dynamics operate on multi-year timescales, a finding which likely applies to other ecosystems, with implications for study design and interpretation. Understanding the drivers and controls of bacterial communities on long time scales would improve both our knowledge of fundamental properties of bacterial communities, and our ability to predict community states. In this specific ecosystem, bog lakes play a disproportionately large role in global carbon cycling, and the information presented here may ultimately help refine carbon budgets for these lakes. Finally, all data and code in this study are publicly available. We hope that this will serve as a resource to anyone seeking to answer their own microbial ecology questions using a multi-year time series.

microbiology↗