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Soil microbiomes are heterogeneous, complex microbial communities. Metagenomic analysis is generating vast amounts of data, creating immense challenges in sequence assembly and analysis. Although advances in technology have resulted in the ability to easily collect large amounts of sequence data, soil samples containing thousands of unique taxa are often poorly characterized. These challenges reduce the usefulness of genome-resolved metagenomic (GRM) analysis seen in other fields of microbiology, such as the creation of high quality metagenomic assembled genomes and the adoption of genome scale modeling approaches. The absence of these resources restricts the scale of future research, limiting hypothesis generation and the predictive modeling of microbial communities. Creating publicly available databases of soil MAGs, similar to databases produced for other microbiomes, has the potential to transform scientific insights about soil microbiomes without requiring the computational resources and domain expertise for assembly and binning.

While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils, owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the United States to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi, Nitrospirae, Euryarchaeota, and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low-nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments.IMPORTANCE Soil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the United States, we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored communities distinct from those of the more commonly studied surface horizons. Most notably, we found that the candidate phylum Dormibacteraeota (formerly AD3) was often dominant in subsurface soils, and we used genomes from uncultivated members of this group to identify why these taxa are able to thrive in such resource-limited environments. Simply digging deeper into soil can reveal a surprising number of novel microbes with unique adaptations to oligotrophic subsurface conditions.

While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils, owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the United States to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi, Nitrospirae, Euryarchaeota, and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low-nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments.IMPORTANCE Soil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the United States, we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored communities distinct from those of the more commonly studied surface horizons. Most notably, we found that the candidate phylum Dormibacteraeota (formerly AD3) was often dominant in subsurface soils, and we used genomes from uncultivated members of this group to identify why these taxa are able to thrive in such resource-limited environments. Simply digging deeper into soil can reveal a surprising number of novel microbes with unique adaptations to oligotrophic subsurface conditions.

Mineral weathering is a balanced interplay among physical, chemical, and biological processes. Fundamental knowledge gaps exist in characterizing the biogeochemical mechanisms that transform microbe-mineral interfaces at submicron scales, particularly in complex field systems. Our objective was to develop methods targeting the nanoscale by using high-resolution microscopy to assess biological and geochemical drivers of weathering in natural settings. Basalt, granite, and quartz (53-250 µm) were deployed in surface soils (10 cm) of three ecosystems (semiarid, subhumid, humid) for one year. We successfully developed a reference grid method to analyze individual grains using: (1) helium ion microscopy to capture micron to sub-nanometer imagery of mineral-organic interactions; and (2) scanning electron microscopy to quantify elemental distribution on the same surfaces via element mapping and point analyses. We detected locations of biomechanical weathering, secondary mineral precipitation, biofilm formation, and grain coatings across the three contrasting climates. To our knowledge, this is the first time these coupled microscopy techniques were applied in the earth and ecosystem sciences to assess microbe-mineral interfaces and in situ biological contributors to incipient weathering.

Rapid changes in climate and land use and the resulting shifts in species distributions and ecosystem functions have motivated the development of the National Ecological Observatory Network (NEON). Integrating across spatial scales from ground sampling to remote sensing, NEON will provide data for users to address ecological responses to changes in climate, land use, and species invasion across the United States for at least 30 years. Although NEON remote sensing and tower sensor elements are relatively well known, the biological measurements are not. This manuscript describes NEON terrestrial sampling, which targets organisms across a range of generation and turnover times, and a hierarchy of measurable biological states. Measurements encompass species diversity, abundance, phenology, demography, infectious disease, ecohydrology, and biogeochemistry. The continental‐scale sampling requires collection of comparable and calibrated data using transparent methods. Data will be publicly available in a variety of formats and suitable for integration with other long‐term efforts. NEON will provide users with the data necessary to address large‐scale questions, challenge current ecological paradigms, and forecast ecological change.

This report details the outcome the first meeting of the Earth Microbiome Project to discuss sample selection and acquisition. The meeting, held at the Argonne National Laboratory on Wednesday October 6(th) 2010, focused on discussion of how to prioritize environmental samples for sequencing and metagenomic analysis as part of the global effort of the EMP to systematically determine the functional and phylogenetic diversity of microbial communities across the world.

Tropical forests are important reservoirs of biodiversity (1), but the processes that maintain this diversity remain poorly understood (2). The Janzen-Connell hypothesis (3,4) suggests that specialized natural enemies such as insect herbivores and fungal pathogens maintain high diversity by elevating mortality when plant species occur at high density (negative density dependence; NDD). NDD has been detected widely in tropical forests (5-9), but the prediction that NDD caused by insects and pathogens has a community-wide role in maintaining tropical plant diversity remains untested. We show experimentally that changes in plant diversity and species composition are caused by fungal pathogens and insect herbivores. Effective plant species richness increased across the seed-to-seedling transition, corresponding to large changes in species composition (5). Treating seeds and young seedlings with fungicides significantly reduced the diversity of the seedling assemblage, consistent with the Janzen-Connell hypothesis. Although suppressing insect herbivores using insecticides did not alter species diversity, it greatly increased seedling recruitment and caused a marked shift in seedling species composition. Overall, seedling recruitment was significantly reduced at high conspecific seed densities and this NDD was greatest for the species that were most abundant as seeds. Suppressing fungi reduced the negative effects of density on recruitment, confirming that the diversity-enhancing effect of fungi is mediated by NDD. Our study provides an overall test of the Janzen-Connell hypothesis and demonstrates the crucial role that insects and pathogens have both in structuring tropical plant communities and in maintaining their remarkable diversity., Understanding the mechanisms that allow species to coexist in natural ecosystems is one of the most enduring questions in community ecology. The key challenge is to identify how competitive exclusion [...]

Forest succession is a key driver of plant communities and understanding succession is central to forest restoration. Currently, the information on the response of the microbial community to the forest succession process, however, is limited. In the present study, we investigated the dynamics of the soil bacterial community in three forest types undergoing succession caused by pine wilt disease, representing the initial pine forest, gradual mixed pine and broadleaved forest, and eventual broadleaved forest, using Illumina MiSeq coupled with Functional Annotation of Prokaryotic Taxa (FAPROTAX) analysis.The results showed that the soil pH, contents of soil organic carbon (SOC) and soil total nitrogen (TN) increased after the occurrence of initial succession and differed among the forest sites. The mixed pine forest had significantly higher bacteria biomass (p < 0.05), whereas, the total microbial biomass did not differ during the succession. The bacterial community diversity and richness increased significantly following the succession process (p < 0.05). Proteobacteria, Actinobacteria, Acidobacteria and Bacteroidetes were the dominant phyla across the succession, in which the abundance of Bacteroidetes significantly increased (p < 0.05), whereas, Planctomycetes, WPS‐2 and Burkholder decreased in abundance after succession occurred (p < 0.05).The three forests formed distinct bacterial community structures during the succession (p < 0.05), whereas, only two functional structures were clustered, in which the mixed and pure broadleaved forest did not differ. The dominant functional groups involved in the C cycle in the initial pure pine forest were replaced gradually by the groups involved in N and S cycles following the subsequent succession. The soil pH, soil TN and SOC were the most important factors affecting the bacterial community and functional structures during the succession.These results indicate that the bacterial community and function shift drastically in the early stages of succession, which reflects the changes in ecological environment caused by succession. The findings provide useful information to better understand the response of microbes to natural forest disturbance and highlight the importance of microbes during forest succession. A free Plain Language Summary can be found within the Supporting Information of this article. [ABSTRACT FROM AUTHOR]

Increased availability of soil phosphorus (P) has recently been recognised as an underlying driving factor for the positive relationship between plant diversity and ecosystem function. The effects of plant diversity on the bioavailable forms of P involved in biologically mediated rhizospheric processes and how the link between plant and soil microbial diversity facilitates soil P bioavailability, however, remain poorly understood.This study quantified four forms of bioavailable P (CaCl2‐P, citric‐P, enzyme‐P and HCl‐P) in mature subtropical forests using a novel biologically based approach, which emulates how rhizospheric processes influence the release and supply of available P. Soil microbial diversity was measured by Illumina high‐throughput sequencing.Our results suggest that tree species richness significantly affects soil microbial diversity (p < 0.05), increases litter decomposition, fine‐root biomass and length and soil organic carbon and thus increases the four forms of bioavailable P. A structural equation model that links plants, soil microbes and P forms indicated that soil bacterial and fungal diversity play dominant roles in mediating the effects of tree species richness on soil P bioavailability.An increase in the biodiversity of plants, soil bacteria and fungi could maintain soil P bioavailability and alleviate soil P limitations. Our results imply that biodiversity strengthens plant and soil feedback and increases P recycling. A plain language summary is available for this article. [ABSTRACT FROM AUTHOR]

Ecosystem processes and the organisms involved are generally limited by the availability of one or more elements in soil, an important phenomenon to consider for our understanding of ecosystem functioning and future changes. Especially in tropical forests, typically growing on nutrient depleted soils, nitrogen (N), phosphorus (P) or other limitations are assumed. However, large‐scale nutrient manipulation experiments revealed complex site‐specific patterns and several authors raised the need for novel approaches to reveal deeper mechanistic insights on limitation patterns, especially concerning soil microbial activity.In order to gain such deeper knowledge, based on a short review of previous small‐scale studies focusing on soil micro‐organisms, we developed an experimental approach which controls for common biases, including indirect treatment effects, addition of co‐elements or nutrient pulses. Using this technique, we tested the hypotheses that fungi growing in tropical forest soils are mainly limited by P and that N versus P limitations shift along an altitudinal gradient.Mesh bags of 38 μm filled with sand were amended with weak ion exchange resins loaded with N, P or potassium (K) and buried underneath the litter layer at three altitudinal sites in southern Ecuador. After a period of four months, the in‐growth of fungal hyphae was quantified, phospholipid fatty acids were analysed for a subset of samples, and chemical properties were determined.In line with the first hypothesis, hyphal abundance was increased in P‐amended mesh bags, indicating P limitation. However, this pattern was not significantly shifted along the altitudinal gradient. By contrast, N addition increased hyphal abundance at the lowest site, compared to significant reductions at 2,000 and 3,000 m—not only in fungi but also in bacterial abundance as indicated by PLFA analyses, contradicting common soil‐age hypotheses. Decreased nutrient immobilization and fungal in‐growth at higher elevations suggest slow microbial activity, including nitrification, which may have caused toxic ammonium accumulation.The experimental design offers a promising tool to provide more mechanistic and soil‐focused analyses specifically targeting microbes, which in this system strongly supported the hypothesis of primary fungal P limitation in tropical forest soils. A plain language summary is available for this article. [ABSTRACT FROM AUTHOR]

Maternal effects (i.e. trans‐generational plasticity) and soil legacies generated by drought and plant diversity can affect plant performance and alter nutrient cycling and plant community dynamics. However, the relative importance and combined effects of these factors on plant growth dynamics remain poorly understood.We used soil and seeds from an existing plant diversity and drought manipulation field experiment in temperate grassland to test maternal, soil drought and diversity legacy effects, and their interactions, on offspring plant performance of two grassland species (Alopecurus pratensis and Holcus lanatus) under contrasting glasshouse conditions.Our results showed that drought soil legacy effects eclipsed maternal effects on plant biomass. Drought soil legacy effects were attributed to changes in both abiotic (i.e. nutrient availability) and biotic soil properties (i.e. microbial carbon and enzyme activity), as well as plant root and shoot atom 15N excess. Further, plant tissue nutrient concentrations and soil microbial C:N responses to drought legacies varied between the two plant species and soils from high and low plant diversity treatments. However, these diversity effects did not affect plant root or shoot biomass.These findings demonstrate that while maternal effects resulting from drought occur in grasslands, their impacts on plant performance are likely minor relative to drought legacy effects on soil abiotic and biotic properties. This suggests that soil drought legacy effects could become increasingly important drivers of plant community dynamics and ecosystem functioning as extreme weather events become more frequent and intense with climate change. A plain language summary is available for this article. [ABSTRACT FROM AUTHOR]

The enemy‐induced Janzen–Connell (JC) effect, a classic model invoking conspecific negative density dependence (CNDD) and distance dependence, is a primary biodiversity maintenance hypothesis. Yet, conflicting evidence for the JC effect leads to disagreement about its role in maintaining forest diversity.We focus this review on soil‐borne pathogens, which are the primary agent inducing the JC effect in many forest ecosystems. Although the test of the pathogen‐induced JC effect in ecology critically rests on the seedling mortality caused by soil pathogens, what has not been explicitly explored in the early literature but has increasingly received attention is the long‐recognized fact that the environment can alter virulence of pathogens and host susceptibility (thus pathogen–host interactions), as predicted by the classic disease triangle framework enlightened by pathology research in agricultural systems.Here, following the disease triangle framework we review evidence on how the pathogen‐induced JC effect may be contingent on context (e.g. environmental conditions, pathogen inoculum load and genetic divergence in host and pathogen populations). The reviewed evidence reveals and clarifies the conditions where pathogens may or may not cause disease to hosts, thus contributing to reconciling the inconsistent results about the pathogen‐induced JC effect in the literature. The context dependence of the disease triangle predicts that the pathogen‐induced JC effect would change under global change.Gaining insights from evidence that the pathogen‐induced JC effect is context‐dependent, we suggest that future tests on the JC hypothesis be conducted under the framework of disease triangle, and we stress the necessity by controlling the effect of context factors on plant–pathogen interactions when testing for the JC effect. We conclude the review by proposing three lines of future research for testing the importance of the JC effect in maintaining global forest tree species diversity, with a particular emphasis on testing the effect of global warming on the strength of pathogen–host interactions for better predicting changes of forest biodiversity under climate change. A plain language summary is available for this article. [ABSTRACT FROM AUTHOR]

Livestock grazing has been shown to alter the structure and functions of grassland ecosystems. It is well acknowledged that grazing pressure is one of the strongest drivers of ecosystem‐level effects of grazing, but few studies have assessed how grazing pressure impacts grassland biodiversity and ecosystem multifunctionality (EMF).Here, we assessed how different metrics of biodiversity (i.e., plants and soil microbes) and EMF responded to seven different grazing treatments based on an 11‐year field experiment in semi‐arid Inner Mongolian steppe.We found that soil organic carbon, plant‐available nitrogen and plant functional diversity all decreased even at low grazing pressure, while above‐ground primary production and bacterial abundance decreased only at high levels of grazing pressure.Structural equation models revealed that EMF was driven by direct effects of grazing, rather than the effects of grazing on plant or microbial community composition. Grazing effects on plant functional diversity and soil microbial abundance did have moderate effects on EMF, while plant richness did not.Synthesis. Our results showed ecosystem functions differ in their sensitivity to grazing pressure, requiring a low grazing threshold to achieve multiple goals in the Eurasian steppe. A plain language summary is available for this article. Plain Language Summary [ABSTRACT FROM AUTHOR]

Due to intensifying human disturbance, over half of the world's tropical forests are reforested or afforested secondary forests or plantations. Understanding the resilience of carbon (C) stocks in these forests, and estimating the extent to which they can provide equivalent carbon (C) sequestration and stabilization to the old growth forest they replace, is critical for the global C balance., In this study, we combined estimates of biomass C stocks with a detailed assessment of soil C pools in bare land, Eucalyptus plantation, secondary forest and natural old-growth forest after over 50 years of forest restoration in a degraded tropical region of South China. We used isotope studies, density fractionation and physical fractionation to determine the age and stability of soil C pools at different soil depths., After 52 years, the secondary forests had equivalent biomass C stocks to natural forest, whereas soil C stocks were still much higher in natural forest (97.42 t/ha) than in secondary forest (58.75 t/ha) or Eucalyptus plantation (38.99 t/ha) and lowest in bare land (19.9 t/ha). Analysis of δ13C values revealed that most of the C in the soil surface horizons in the secondary forest was new C, with a limited increase of more recalcitrant old C, and limited accumulation of C in deeper soil horizons. However, occlusion of C in microaggregates in the surface soil layer was similar across forested sites, which suggests that there is great potential for additional soil C sequestration and stabilization in the secondary forest and Eucalyptus plantation., Collectively, our results demonstrate that reforestation on degraded tropical land can restore biomass C and surface soil C stocks within a few decades, but much longer recovery times are needed to restore recalcitrant C pools and C stocks at depth. Repeated harvesting and disturbance in rotation plantations had a substantial negative impact on the recovery of soil C stocks. We suggest that current calculations of soil C in secondary tropical forests (e.g. IPCC Guidelines for National Greenhouse Gas Inventories) could overestimate soil C sequestration and stabilization levels in secondary forests and plantations., A is available for this article. [ABSTRACT FROM AUTHOR]