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Adaptation of soil microbes due to warming from climate change has been observed, but it remains unknown what microbial growth traits are adaptive to warming. We studied bacterial isolates from the Harvard Forest Long-Term Ecological Research site, where field soils have been experimentally heated to 5°C above ambient temperature with unheated controls for thirty years. We hypothesized that Alphaproteobacteria from warmed plots have (1) less temperature sensitive growth rates; (2) higher optimum growth temperatures; and (3) higher maximum growth temperatures compared to isolates from control plots. We made high-throughput measurements of bacterial growth in liquid cultures over time and across temperatures from 22-37°C in 2-3°C increments. We estimated growth rates by fitting Gompertz models to the growth data. Temperature sensitivity of growth rate, optimum growth temperature, and maximum growth temperature were estimated by the Ratkowsky 1983 model and a modified Macromolecular Rate Theory (MMRT) model. To determine evidence of adaptation, we ran phylogenetic generalized least squares tests on isolates from warmed and control soils. Our results showed evidence of adaptation of higher optimum growth temperature of bacterial isolates from heated soils. However, we observed no evidence of adaptation of temperature sensitivity of growth and maximum growth temperature. Our project begins to capture the shape of the temperature response curves, but illustrates that the relationship between growth and temperature is complex and cannot be limited to a single point in the biokinetic range.ImportanceSoils are the largest terrestrial carbon sink and the foundation of our food, fiber, and fuel systems. Healthy soils are carbon sinks, storing more carbon than they release. This reduces the amount of carbon dioxide released to the atmosphere and buffers against climate change. Soil microbes drive biogeochemical cycling and contribute to soil health through organic matter breakdown, plant growth promotion, and nutrient distribution. In this study, we determined how soil microbial growth traits respond to long-term soil warming. We found that bacterial isolates from warmed plots showed evidence of adaptation of increased optimum growth temperature. This suggests that increased microbial biomass and growth relative to respiration in a warming world should result in greater carbon storage. As temperatures increase, greater microbial activity may help reduce the soil carbon feedback loop. Our results provide insight on how atmospheric carbon cycling and soil health may respond in a warming world.

Evolutionary responses to anthropogenic climate change are irreversible and largely uncaptured by climate models. Below-ground carbon transformations represent an important natural mitigation solution, but novel adaptive traits may alter microbial climate feedback mechanisms. To better define microbial evolutionary responses to warming, we study microorganisms from an ongoingin situsoil warming experiment at the Harvard Forest Long-term Ecological Research (LTER) site where, for over three decades, soils are continuously heated 5 ºC above ambient temperatures. We hypothesize that across generations of chronic warming, genomic signatures within diverse bacterial lineages reflect adaptations related to growth and carbon utilization. From our culture collection of soil bacteria isolated from experimental heated and control plots, we sequenced genomes representing taxa dominant in soil communities and sensitive to warming, including independent lineages of Alphaproteobacteria, Actinobacteria, and Betaproteobacteria. We investigated differences in genomic attributes and patterns of functional gene content to identify genetic signatures of adaptation. Comparative pangenomics revealed differently abundant gene clusters with functional annotations related to carbon and nitrogen metabolism. We also observe differences in genome-wide codon usage bias between heated and control genomes, suggesting potential adaptive traits related to growth or growth efficiency. Together, these data illustrate the emergence of diverse lineage-specific adaptive traits as well as common ecological-evolutionary microbial responses to climate change.

Microbes are responsible for cycling carbon (C) through soils, and the predictions of how soil C stocks change with warming are highly sensitive to the assumptions made about the mechanisms controlling the microbial physiology response to climate warming. Two mechanisms, microbial thermal-acclimation and changes in the quantity and quality of substrates available for microbial metabolism have been suggested to explain the long-term warming impact on microbial physiology. Yet studies disentangling these two mechanisms are lacking. To resolve the drivers of changes in microbial physiology in response to long-term warming, we sampled soils from 13- and 28-year old soil warming experiments in different seasons. We performed short-term laboratory incubations across a range of temperatures to measure the relationship between temperature sensitivity of physiology (growth, respiration, carbon use efficiency and extracellular enzyme activity) and the chemical composition of soil organic matter. We observed apparent thermal acclimation in microbial processes important for C cycling, but only when warming had exacerbated the seasonally-induced, already small soil organic matter pools. Irrespective of warming, greater quantity and quality of soil carbon enhanced the extracellular enzymatic pool and its temperature sensitivity. We suggest that fresh litter input into the system seasonally cancels apparent thermal acclimation of C-cycling processes. Our findings reveal that long-term warming has indirectly affected microbial physiology via reduced C availability in this system, implying that earth system models including these negative feedbacks may be best suited to describe long-term warming impact in soils.

House flies are disease vectors, carrying human pathogens which include Escherichia coli and Vibrio cholera. To explore the use of chitosan as a bioinsecticide, we evaluated the effects of a chitosan-amended diet on Musca domestica (house fly). We first conducted longevity experiments to understand the impact of chitosan on house fly longevity. We confirmed that chitosan diet amendment is associated with reduced longevity and that this is not due to starvation. We then extracted fly microbiome DNA and used 16S ribosomal RNA gene amplicon sequencing and quantitative PCR to assess the composition and load of the microbiome for flies fed chitosan-amended diets compared to controls. Diversity of the chitosan-fed fly microbiomes was lower than the control, with significant dissimilarities in community composition. Chitosan-fed flies showed lower Ralstonia relative abundance but increased relative abundance of Serratia. Both control and chitosan-fed flies had highly uneven communities, but the control flies were dominated by genera Ralstonia and Providencia, while the chitosan-fed flies were dominated by genera Serratia, Kosakonia, and Providencia. Contrary to our expected results, chitosan-fed flies also contained 56% more bacteria compared to controls. Gut microbiome changes appear to result from chitinolytic bacteria becoming more relatively abundant, and our results suggest that chitosan-amended diet alters the house fly microbiome resulting in higher fly mortality.

We report the draft genome sequence of Leifsonia poae strain BS71. This bacterium was isolated from a low soil moisture content model soil microcosm inoculated with forest soil that had been subject to chronic warming.

Small genes (40,000 small-gene families in ~2.3 million phage genome contigs. We find that small genes in phage genomes are approximately 3-fold more prevalent than in host prokaryotic genomes. Our approach enriches for small genes that are translated in microbiomes, suggesting the small genes identified are coding. More than 9,000 families encode potentially secreted or transmembrane proteins, more than 5,000 families encode predicted anti-CRISPR proteins, and more than 500 families encode predicted antimicrobial proteins. By combining homology and genomic-neighborhood analyses, we reveal substantial novelty and diversity within phage biology, including small phage genes found in multiple host phyla, small genes encoding proteins that play essential roles in host infection, and small genes that share genomic neighborhoods and whose encoded proteins may share related functions.

The largest terrestrial carbon sink on earth is soil carbon stocks. As the climate changes, the rate at which the Earth’s climate warms depends in part on the persistence of soil organic carbon. Microbial turnover forms the backbone of soil organic matter (SOM) formation and it has been recently proposed that SOM molecular complexity is a key driver of stability. Despite this, the links between microbial diversity, chemical complexity and biogeochemical nature of SOM remain missing. Here we tested the hypotheses that distinct microbial communities shape the composition of SOM, and microbial-derived SOM has distinct decomposition potential depending on its community of origin. We inoculated microbial communities of varying diversities into a model soil matrix amended with simple carbon (cellobiose) and measured the thermal stability of the resultant SOM. Using a Rock-Eval® ramped thermal analysis, we found that microbial community composition drives the chemical fingerprint of soil carbon. While diversity was not a driver of SOM composition, bacteria-only communities lead to more thermally labile soil C pools than communities with bacteria and fungi. Our results provide direct evidence for a link between microbial community structure, SOM composition, and thermal stability. This evidence demonstrates the relevance of soil microorganisms in building persistent SOM stocks.

Climate change has the potential to destabilize the Earth's massive terrestrial carbon (C) stocks, but the degree to which models project this destabilization to occur depends on the kinds and complexities of microbial processes they simulate. Of particular note is carbon use efficiency (CUE), which determines the fraction of C processed by microbes that is anabolized into microbial biomass rather than lost to the atmosphere and soil as carbon dioxide and extracellular products. The temperature sensitivity of CUE is often modeled as an intrinsically fixed (homogeneous) property of the community, which contrasts with empirical data and has unknown impacts on projected changes to the soil C cycle under global warming. We used the Decomposition Model of Enzymatic Traits (DEMENT) – which simulates taxon-level litter decomposition dynamics – to explore the effects of introducing organism-level heterogeneity into the CUE response to temperature for decomposition of leaf litter under 5 ∘C of warming. We found that allowing the CUE temperature response to differ between taxa facilitated increased loss of litter C, unless fungal taxa were specifically restricted to decreasing CUE with temperature. Litter C loss was exacerbated by variable and elevated CUE at higher temperature, which effectively lowered costs for extracellular enzyme production. Together these results implicate a role for diversity of taxon-level CUE responses in driving the fate of litter C in a warmer world within DEMENT, which should be explored within the framework of additional model structures and validated with empirical studies.

A recent paper by Martiny argues that “high proportions” of bacteria in diverse Earth environments have been cultured. Here we reanalyze a portion of the data in that paper, and argue that the conclusion is based on several technical errors, most notably a calculation of sequence similarity that does not account for sequence gaps, and the reliance on 16S rRNA gene amplicons that are known to be biased towards cultured organisms. We further argue that the paper is also based on a conceptual error: namely, that sequence similarity cannot be used to infer “culturability” because one cannot infer physiology from 16S rRNA gene sequences. Combined with other recent, more reliable studies, the evidence supports the conclusion that most bacterial and archaeal taxa remain uncultured.

Humans are inextricably linked to each other and our natural world, and microorganisms lie at the nexus of those interactions. Microorganisms form genetically flexible, taxonomically diverse, and biochemically rich communities, i.e., microbiomes that are integral to the health and development of macroorganisms, societies, and ecosystems. Yet engagement with beneficial microbiomes is dictated by access to public resources, such as nutritious food, clean water and air, safe shelter, social interactions, and effective medicine. In this way, microbiomes have sociopolitical contexts that must be considered. The Microbes and Social Equity (MSE) Working Group connects microbiology with social equity research, education, policy, and practice to understand the interplay of microorganisms, individuals, societies, and ecosystems. Here, we outline opportunities for integrating microbiology and social equity work through broadening education and training; diversifying research topics, methods, and perspectives; and advocating for evidence-based public policy that supports sustainable, equitable, and microbial wealth for all.

Correction to: Nature Microbiology https://doi.org/10.1038/s41564-020-0733-x , published online 8 June 2020. In the version of this Consensus Statement originally published, Pablo Yarza was mistakenly not included in the author list. Also, in Supplementary Table 1, Alexander Jaffe was missing from the list of endorsees. These errors have now been corrected and the updated Supplementary Table 1 is available online.

Here, we present the draft genome sequence of a novel species of the genus Singulisphaera (phylum Planctomycetes, family Isosphaeraceae) isolated from soil. Singulisphaera sp. strain GP187 has a relatively large mobilome and numerous novel genes that may contribute to the production of bioactive molecules.

Here, we present the draft genome sequence of a novel species of the genus Singulisphaera (phylum Planctomycetes , family Isosphaeraceae ) isolated from soil. Singulisphaera sp. strain GP187 has a relatively large mobilome and numerous novel genes that may contribute to the production of bioactive molecules.

Frankiaceae are bacterial endosymbionts that are also found free-living in soil. Here, we present the genome sequences of two novel bacterial members of the order Frankiales , class Actinobacteria , isolated from temperate terrestrial forest soils. The genomes for MT45 and GAS493 indicate a genetic capacity for carbohydrate degradation but not nitrogen fixation.

Lignin is the second most abundant carbon polymer on earth and despite having more fuel value than cellulose, it currently is considered a waste byproduct in many industrial lignocellulose applications. Valorization of lignin relies on effective and green methods of de-lignification, with a growing interest in the use of microbes. Here we investigate the physiology and molecular response of the novel facultative anaerobic bacterium, Tolumonas lignolytica BRL6-1, to lignin under anoxic conditions. Physiological and biochemical changes were compared between cells grown anaerobically in either lignin-amended or unamended conditions. In the presence of lignin, BRL6-1 accumulates higher biomass and has a shorter lag phase compared to unamended conditions, and 14% of the proteins determined to be significantly higher in abundance by log2 fold-change of 2 or greater were related to Fe(II) transport in late logarithmic phase. Ferrozine assays of the supernatant confirmed that Fe(III) was bound to lignin and reduced to Fe(II) only in the presence of BRL6-1, suggesting redox activity by the cells. LC-MS/MS analysis of the secretome showed an extra band at 20 kDa in lignin-amended conditions. Protein sequencing of this band identified a protein of unknown function with homology to enzymes in the radical SAM superfamily. Expression of this protein in lignin-amended conditions suggests its role in radical formation. From our findings, we suggest that BRL6-1 is using a protein in the radical SAM superfamily to interact with the Fe(III) bound to lignin and reducing it to Fe(II) for cellular use, increasing BRL6-1 yield under lignin-amended conditions. This interaction potentially generates organic free radicals and causes a radical cascade which could modify and depolymerize lignin. Further research should clarify the extent to which this mechanism is similar to previously described aerobic chelator-mediated Fenton chemistry or radical producing lignolytic enzymes, such as lignin peroxidases, but under anoxic conditions.

8 pages, 2 figures, 1 table, 2 boxes, supplementary information https://doi.org/10.1038/s41564-020-0733-x.-- Author Correction: Roadmap for naming uncultivated Archaea and Bacteria: n the version of this Consensus Statement originally published, Pablo Yarza was mistakenly not included in the author list. Also, in Supplementary Table 1, Alexander Jaffe was missing from the list of endorsees. These errors have now been corrected and the updated Supplementary Table 1 is available online, The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as ‘type material’, thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity, Support for this effort was provided by the National Science Foundation (grant no. DEB-1841658). We extend deep appreciation to all who attended the Microbial Taxonomy 2018 seminars, the Microbial Systematics for the Next Decade workshop held in Hood River, Oregon, USA, in October 2018, and those that participated in subsequent, With the funding support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), of the Spanish Research Agency (AEI)

Lignin is the second most abundant carbon polymer on earth and despite having more fuel value than cellulose, it currently is considered a waste byproduct in many industrial lignocellulose applications. Valorization of lignin relies on effective and green methods of delignification, with a growing interest in the use of microbes. Here we investigate the physiology and lignin biotransformation mechanisms of the novel facultative anaerobic bacterium,Tolumonas lignolyticaBRL6-1, under anoxic conditions. Physiological and biochemical changes were compared between cells grown anaerobically in either lignin-amended or unamended conditions. In the presence of lignin, BRL6-1 had a higher biomass and shorter lag phase compared to unamended conditions, and 14% of the proteins determined to be significantly higher in abundance by log2fold-change of 2 or greater were related to Fe(II) transport in early exponential phase. Ferrozine assays of the supernatant (

Climate and the carbon cycle It is still not clear how global warming will affect the global carbon cycle, either in terms of the magnitude of the effect or even its sign. Help in answering that question will come from long-term field-based experiments designed to explore carbon cycle-climate feedbacks in an ecosystem context. Melillo et al. performed a 26-year soil-warming experiment in a mid-latitude hardwood forest (see the Perspective by Metcalfe). Warming has resulted in a complex pattern of net carbon loss from the soil. These results support projections of a long-term, positive carbon feedback from similar ecosystems as the world warms. Science , this issue p. 101 ; See also p. 41

As earth's climate continues to warm, it is important to understand how the capacity of terrestrial ecosystems to retain carbon (C) will be affected. We combined measurements of microbial activity with the concentration, quality, and physical accessibility of soil carbon to microorganisms to evaluate the mechanisms by which more than two decades of experimental warming has altered the carbon cycle in a Northeast US temperate deciduous forest. We found that concentrations of soil organic matter were reduced in both the organic and mineral soil horizons. The molecular composition of the carbon was altered in the mineral soil with significant reductions in the relative abundance of polysaccharides and lignin, and an increase in lipids. Mineral-associated organic matter was preferentially depleted by warming in the top 3 cm of mineral soil. We found that potential extracellular enzyme activity per gram of soil at a common temperature was generally unaffected by warming treatment. However, by measuring potential extracellular enzyme activities between 4 and 30 °C, we found that activity per unit microbial biomass at in-situ temperatures was increased by warming. This was associated with a tendency for microbial biomass to decrease with warming. These results indicate that chronic warming has reduced soil organic matter concentrations, selecting for a smaller but more active microbial community increasingly dependent on mineral-associated organic matter.

Climate change has the potential to destabilize the Earth’s massive terrestrial carbon (C) stocks, but the degree to which models project this destabilization to occur depends on the kinds and complexities of microbial processes they simulate. Of particular note is carbon use efficiency (CUE), which determines the fraction of C processed by microbes that is anabolized into microbial biomass rather than being lost to the atmosphere as carbon dioxide. The temperature sensitivity of CUE is often modeled as a homogeneous property of the community, which contrasts with empirical data and has unknown impacts on projected changes to the soil carbon cycle under global warming. We used the DEMENT model – which simulates taxon-level litter decomposition dynamics – to explore the effects of introducing organism-level heterogeneity into the CUE response to temperature for decomposition of leaf litter under 5 °C of warming. We found that allowing CUE temperature response to differ between taxa facilitated increased loss of litter C, unless fungal taxa were specifically restricted to decreasing CUE with temperature. Increased loss of litter C was observed when the growth of a larger microbial biomass pool was fueled by higher community-level average CUE at higher temperature in the heterogeneous microbial community, with effectively lower costs for extracellular enzyme production. Together these results implicate a role for diversity of taxon-level CUE responses in driving the fate of litter C in a warmer world.

The complete genome sequence of the gammaproteobacterial isolate Serratia quinivorans 124R consists of 5 Mb over 2 scaffolds and a G+C content of 52.85%. Genes relating to aromatic metabolism reflect its isolation on organosolv lignin as a sole carbon source under anoxic conditions as well as the potential for lignin biorefinery applications.

A recent paper by Martiny argues that "high proportions" of bacteria in diverse Earth environments have been cultured. Here we reanalyze a portion of the data in that paper, and argue that the conclusion is based on several technical errors, most notably a calculation of sequence similarity that does not account for sequence gaps, and the reliance on 16S rRNA gene amplicons that are known to be biased towards cultured organisms. We further argue that the paper is also based on a conceptual error: namely, that sequence similarity cannot be used to infer "culturability" because one cannot infer physiology from 16S rRNA gene sequences. Combined with other recent, more reliable studies, the evidence supports the conclusion that most bacterial and archaeal taxa remain uncultured.

1AbstractHow microbes allocate carbon to growth vs. respiration plays a central role in determining the ability of soil to retain carbon. This carbon use efficiency (CUE) is increasingly measured using the18O-H2O method, in which heavy oxygen incorporated into DNA is used to estimate growth. Here we evaluated the validity of some of the assumptions of this method using a literature search, and then tested how violating them affected estimates of the growth component of carbon use efficiency in soil. We found that the18O method is consistently sensitive to assumptions made about oxygen sources to DNA, but that the effect of other assumptions depends on the microbial community present. We provide an example for how the tools developed here may be used with observed CUE values, and demonstrate that the original conclusions drawn from the data remain robust in the face of methodological bias. Our results lay the foundation for a better understanding of the consequences to the18O method underlying assumptions. Future studies can use the approach developed here to identify how different incubation conditions and/or treatments might bias its CUE estimates and how trustworthy their results are. Further wet-lab work dissecting the assumptions of the18O method in soil will help justify the scenarios under which it is reasonable to trust its results.

Climate warming can affect the temperature sensitivity of microbial activity and growth efficiency, possibly explained by changes to microbially unavailable carbon (C) protected within in soil aggregates. We assessed physical protection by crushing macroaggregates (250–2000 μm) and microaggregates (

As Earth's climate warms, soil carbon pools and the microbial communities that process them may change, altering the way in which carbon is recycled in soil. In this study, we used a combination of metagenomics and bacterial cultivation to evaluate the hypothesis that experimentally raising soil temperatures by 5°C for 5, 8, or 20 years increased the potential for temperate forest soil microbial communities to degrade carbohydrates. Warming decreased the proportion of carbohydrate-degrading genes in the organic horizon derived from eukaryotes and increased the fraction of genes in the mineral soil associated withActinobacteriain all studies. Genes associated with carbohydrate degradation increased in the organic horizon after 5 years of warming but had decreased in the organic horizon after warming the soil continuously for 20 years. However, a greater proportion of the 295 bacteria from 6 phyla (10 classes, 14 orders, and 34 families) isolated from heated plots in the 20-year experiment were able to depolymerize cellulose and xylan than bacterial isolates from control soils. Together, these findings indicate that the enrichment of bacteria capable of degrading carbohydrates could be important for accelerated carbon cycling in a warmer world.IMPORTANCEThe massive carbon stocks currently held in soils have been built up over millennia, and while numerous lines of evidence indicate that climate change will accelerate the processing of this carbon, it is unclear whether the genetic repertoire of the microbes responsible for this elevated activity will also change. In this study, we showed that bacteria isolated from plots subject to 20 years of 5°C of warming were more likely to depolymerize the plant polymers xylan and cellulose, but that carbohydrate degradation capacity is not uniformly enriched by warming treatment in the metagenomes of soil microbial communities. This study illustrates the utility of combining culture-dependent and culture-independent surveys of microbial communities to improve our understanding of the role changing microbial communities may play in soil carbon cycling under climate change.

Soil microbial carbon use efficiency (CUE) is a combination of growth and respiration, which may respond differently to climate change depending on physical protection of soil carbon (C) and its availability to microbes. In a mid-latitude hardwood forest in central Massachusetts, 27 years of soil warming (+5 °C) has resulted in C loss and altered soil organic matter (SOM) quality, yet the underlying mechanisms remain unclear. Here, we hypothesized that long-term warming reduces physical aggregate protection of SOM, microbial CUE, and its temperature sensitivity. Soil was separated into macroaggregate (250–2000 μm) and microaggregate (

Here, we present the genome sequence of a member of the group I Acidobacteria, Acidipila sp. strain EB88, which was isolated from temperate forest soil., Here, we present the genome sequence of a member of the group I Acidobacteria, Acidipila sp. strain EB88, which was isolated from temperate forest soil. Like many other members of its class, its genome contains evidence of the potential to utilize a broad range of sugars.

Soil microbes are key regulators of Earth's biogeochemical cycles, and their growth, turnover, and efficiency are important controls of organic matter decay and soil carbon (C) storage. A central roadblock to scaling microbial activity is explaining the incongruence between long- and short-term warming responses. In addition to the well-described kinetics which dominate the short-term warming response, the long-term response is also subject to indirect effects, such as substrate availability, soil moisture, and shifts in plant community composition, that influence microbial activity and community dynamics. Here we discuss possible mechanisms of this attenuation, synthesized in the context of five testable hypotheses, presented in order of decreasing current empirical support.

Three strains of a novel Rhizobiales species were isolated from temperate deciduous forest soil in central Massachusetts. Their genomes consist of 9.09 to 10.29 Mb over 3 to 4 scaffolds each and indicate that diverse nitrogenous compounds are used by these organisms.

Three strains of a novel Rhizobiales species were isolated from temperate deciduous forest soil in central Massachusetts. Their genomes consist of 9.09 to 10.29 Mb over 3 to 4 scaffolds each and indicate that diverse nitrogenous compounds are used by these organisms.

Verrucomicrobium sp. strain GAS474 was isolated from the mineral soil of a temperate deciduous forest in central Massachusetts. Here, we present the complete genome sequence of this phylogenetically novel organism, which consists of a total of 3,763,444 bp on a single scaffold, with a 65.8% GC content and 3,273 predicted open reading frames.

Verrucomicrobium sp. strain GAS474 was isolated from the mineral soil of a temperate deciduous forest in central Massachusetts. Here, we present the complete genome sequence of this phylogenetically novel organism, which consists of a total of 3,763,444 bp on a single scaffold, with a 65.8% GC content and 3,273 predicted open reading frames.

The complexity of processes and interactions that drive soil C dynamics necessitate the use of proxy variables to represent soil characteristics that cannot be directly measured (correlative proxies), or that aggregate information about multiple soil characteristics into one variable (integrative proxies). These proxies have proven useful for understanding the soil C cycle, which is highly variable in both space and time, and are now being used to make predictions of the fate and persistence of C under future climate scenarios. However, the C pools and processes that proxies represent must be thoughtfully considered in order to minimize uncertainties in empirical understanding. This is necessary to capture the full value of a proxy in model parameters and in model outcomes. Here, we provide specific examples of proxy variables that could improve decision-making, and modeling skill, while also encouraging continued work on their mechanistic underpinnings. We explore the use of three common soil proxies used to study soil C cycling: metabolic quotient, clay content, and physical fractionation. We also consider how emerging data types, such as genome-sequence data, can serve as proxies for microbial community activities. By examining some broad assumptions in soil C cycling with the proxies already in use, we can develop new hypotheses and specify criteria for new and needed proxies.

Here, we report the high-quality draft genome sequences of four phylogenetically diverse lignocellulose-degrading bacteria isolated from tropical soil ( Gordonia sp., Paenibacillus sp., Variovorax sp., and Vogesella sp.) to elucidate the genetic basis of their ability to degrade lignocellulose. These isolates may provide novel enzymes for biofuel production.