Biology subjects

Cole, J. R.

Publications and source records attributed to Cole, J. R..

4 recordsLinked to original sources

bioRxiv2020

Land-use and forest floor explain prokaryotic metacommunity structuring and spatial turnover in Amazonian forest-to-pasture conversion areas

Advancing extensive cattle production shifts the forest landscape and is considered one of the main drivers against biodiversity conservation in the Brazilian Amazonia. Considering soil as an ecosystem it becomes vital to identify the effects of land-use changes on soil microbial communities, structure, as well as its ecological functions and services. Herein, we explored relationships between land-use, soil types and forest floor (i.e., association between litter, root layer and bulk soil) on the prokaryotic metacommunity structuring in the Western Amazonia. Sites under high anthropogenic pressure were evaluated along a gradient of {+/-} 800 km. Prokaryotic metacommunity are synergistically affected by soil types and land-use systems. Especially, the gradient of soil fertility and land-use shapes the structuring of the metacommunity and determines its composition. Forest-to-pasture conversion increases alpha, beta, and gamma diversities when considering only the prokaryotes from the bulk soil. Beta diversity was significantly higher in all forests when the litter and root layer were taken into account with the bulk soil. Our argumentation is that the forest floor harbors a prokaryotic metacommunity that adds at the regional scale of diversity a spatial turnover hitherto underestimated. Our findings highlight the risks of biodiversity loss and, consequently, the soil microbial diversity maintenance in tropical forests.

microbiology↗

bioRxiv2020

MetaFunPrimer: primer design for targeting genes observed in metagenomes

High throughput primer design is needed to simultaneously design primers for multiple genes of interest, such as a group of functional genes. We have developed MetaFunPrimer, a bioinformatic pipeline to design primer targets for genes of interests, with a prioritization based on ranking the presence of gene targets in references, such as metagenomes. MetaFunPrimer takes inputs of protein and nucleotide sequences for gene targets of interest accompanied by a set of reference metagenomes or genomes for determining genes of interest. Its output is a set of primers that may be used to amplify genes of interest. To demonstrate the usage and benefits of MetaFunPrimer, a total of 78 HT-qPCR primer pairs were designed to target observed ammonia monooxygenase subunit A (amoA) genes of ammonia-oxidizing bacteria (AOB) in 1,550 soil metagenomes. We demonstrate that these primers can significantly improve targeting of amoA-AOB genes in soil metagenomes compared to previously published primers. IMPORTANCEAmplification-based gene characterization allows for sensitive and specific quantification of functional genes. Often, there is a large diversity of genes represented for a function of interest, and multiple primers may be necessary to target associated genes. Current primer design tools are limited to designing primers for only a few genes of interest. MetaFunPrimer allows for high throughput primer design for functional genes of interest and also allows for ranking gene targets by their presence and abundance in environmental datasets. This tool enables high throughput qPCR approaches for characterizing functional genes.

bioinformatics↗

bioRxiv2020

Lower Soil Carbon Loss Due to Persistent Microbial Adaptation to Climate Warming

Soil microbial respiration is an important source of uncertainty in projecting future climate and carbon (C) cycle feedbacks. Despite intensive studies for two decades, the magnitude, direction, and duration of such feedbacks are uncertain, and their underlying microbial mechanisms are still poorly understood. Here we examined the responses of soil respiration and microbial community structure to long-term experimental warming in a temperate grassland ecosystem. Our results indicated that the temperature sensitivity of soil microbial respiration (i.e., Q10) persistently decreased by 12.0{+/-}3.7% across 7 years of warming. Integrated metagenomic and functional analyses showed that microbial community adaptation played critical roles in regulating respiratory acclimation. Incorporating microbial functional gene abundance data into a microbially-enabled ecosystem model significantly improved the modeling performance of soil microbial respiration by 5-19%, compared to the traditional non-microbial model. Model parametric uncertainty was also reduced by 55-71% when gene abundances were used. In addition, our modeling analyses suggested that decreased temperature sensitivity could lead to considerably less heterotrophic respiration (11.6{+/-}7.5%), and hence less soil C loss. If such microbially mediated dampening effects occur generally across different spatial and temporal scales, the potential positive feedback of soil microbial respiration in response to climate warming may be less than previously predicted.

ecology↗

bioRxiv2018

Comparing faster evolving rplB and rpsC versus SSU rRNA for improved microbial community resolution

Many conserved protein-coding core genes are single copy and evolve faster, and thus are more resolving phylogenetic markers than the standard SSU rRNA gene but their use has been precluded by the lack of universal primers. Recent advances in gene targeted assembly methods for large shotgun metagenomes make their use feasible. To evaluate this approach, we compared the variation of two single copy ribosomal protein genes, rplB and rpsC, with the SSU rRNA gene for all completed bacterial genomes in NCBI RefSeq. As expected, among pairwise comparisons of all species that belong to the same genus, 94.9% and 91.0% of the pairs of rplB and rpsC, respectively, showed more variation than did their SSU rRNA gene sequences. We used a gene-targeted assembler, Xander, to assemble rplB and rpsC from shotgun metagenomic data from rhizosphere samples of three crops: corn (annual), and Miscanthus and switchgrass (both perennials). Both protein-coding genes separated all three communities whereas the SSU rRNA gene could only separate the annual from the two perennial communities in ordination analyses. Furthermore, assembled rplB and rpsC yielded significantly higher numbers of OTUs (alpha diversity) than the SSU rRNA gene. These results confirm these faster evolving marker genes offer increased resolution of for comparative microbiome studies.

microbiology↗