Existing Climate Change Will Lead to Pronounced Shifts in the Diversity of Soil Prokaryotes

Soil temperature and fungal diversity jointly modulate soil heterotrophic respiration under short-term warming in the Zoige alpine peatland

Global warming has changed carbon cycling in terrestrial ecosystems, but it remains unclear how climate warming affects soil heterotrophic respiration (Rh). We conducted a field experiment in the Zoige alpine peatland to investigate the mechanism of how short-term warming affects Rh by examining the relationships between plant biomass, soil properties, soil microbial diversity, and functional groups and Rh. Our results showed that warming increased Rh after one growing season of warming. However, warming barely changed the bacterial functional groups involved in the carbon cycle predicted by the functional annotation analysis. According to the Mantel test, NO3- was found to be the primary determinant for bacterial and fungal communities. The results of the Structural Equation Model (SEM) indicate that soil temperature and fungal diversity jointly modulate Rh, suggesting that short-term warming may not affect Rh by altering the structural and functional composition of microorganisms, which provides new insight into the mechanisms of the effects of warming on Rh in terrestrial ecosystems.

The effects of climate and soil depth on living and dead bacterial communities along a longitudinal gradient in Chile

Soil bacterial communities play a critical role in shaping soil stability and formation, exhibiting a dynamic interaction with local climate and soil depth. We employed an innovative DNA separation method to characterize microbial assemblages in low-biomass environments such as deserts and distinguish between intracellular DNA (iDNA) and extracellular DNA (eDNA) in soils. This approach, combined with analyses of physicochemical properties and co-occurrence networks, investigated soil bacterial communities across four sites representing diverse climatic gradients (i.e., arid, semi-arid, Mediterranean, and humid) along the Chilean Coastal Cordillera. The separation method yielded a distinctive unimodal pattern in the iDNA pool alpha diversity, increasing from arid to semi-arid climates and decreasing in humid environments, highlighting the rapid feedback of the iDNA community to increasing soil moisture. In the arid region, harsh surface conditions restrict bacterial growth, leading to peak iDNA abundance and diversity occurring in slightly deeper layers than the other sites. Our findings confirmed the association between specialist bacteria and ecosystem-functional traits. We observed transitions from Halomonas and Delftia, resistant to extreme arid environments, to Class AD3 and the genus Bradyrhizobium, associated with plants and organic matter in humid environments. The distance-based redundancy analysis (dbRDA) analysis revealed that soil pH and moisture were the key parameters that influenced bacterial community variation. The eDNA community correlated slightly better with the environment than the iDNA community. Soil depth was found to influence the iDNA community significantly but not the eDNA community, which might be related to depth-related metabolic activity. Our investigation into iDNA communities uncovered deterministic community assembly and distinct co-occurrence modules correlated with unique bacterial taxa, thereby showing connections with sites and key environmental factors. The study additionally revealed the effects of climatic gradients and soil depth on living and dead bacterial communities, emphasizing the need to distinguish between iDNA and eDNA pools.

Genomic fingerprints of the world's soil ecosystems

Despite the explosion of soil metagenomic data, we lack a synthesized understanding of patterns in the distribution and functions of soil microorganisms. These patterns are critical to predictions of soil microbiome responses to climate change and resulting feedbacks that regulate greenhouse gas release from soils. To address this gap, we assay 1,512 manually curated soil metagenomes using complementary annotation databases, read-based taxonomy, and machine learning to extract multidimensional genomic fingerprints of global soil microbiomes. Our objective is to uncover novel biogeographical patterns of soil microbiomes across environmental factors and ecological biomes with high molecular resolution. We reveal shifts in the potential for (i) microbial nutrient acquisition across pH gradients; (ii) stress-, transport-, and redox-based processes across changes in soil bulk density; and (iii) greenhouse gas emissions across biomes. We also use an unsupervised approach to reveal a collection of soils with distinct genomic signatures, characterized by coordinated changes in soil organic carbon, nitrogen, and cation exchange capacity and in bulk density and clay content that may ultimately reflect soil environments with high microbial activity. Genomic fingerprints for these soils highlight the importance of resource scavenging, plant-microbe interactions, fungi, and heterotrophic metabolisms. Across all analyses, we observed phylogenetic coherence in soil microbiomes-more closely related microorganisms tended to move congruently in response to soil factors. Collectively, the genomic fingerprints uncovered here present a basis for global patterns in the microbial mechanisms underlying soil biogeochemistry and help beget tractable microbial reaction networks for incorporation into process-based models of soil carbon and nutrient cycling.IMPORTANCEWe address a critical gap in our understanding of soil microorganisms and their functions, which have a profound impact on our environment. We analyzed 1,512 global soils with advanced analytics to create detailed genetic profiles (fingerprints) of soil microbiomes. Our work reveals novel patterns in how microorganisms are distributed across different soil environments. For instance, we discovered shifts in microbial potential to acquire nutrients in relation to soil acidity, as well as changes in stress responses and potential greenhouse gas emissions linked to soil structure. We also identified soils with putative high activity that had unique genomic characteristics surrounding resource acquisition, plant-microbe interactions, and fungal activity. Finally, we observed that closely related microorganisms tend to respond in similar ways to changes in their surroundings. Our work is a significant step toward comprehending the intricate world of soil microorganisms and its role in the global climate.

Decoding populations in the ocean microbiome

Understanding the characteristics and structure of populations is fundamental to comprehending ecosystem processes and evolutionary adaptations. While the study of animal and plant populations has spanned a few centuries, microbial populations have been under scientific scrutiny for a considerably shorter period. In the ocean, analyzing the genetic composition of microbial populations and their adaptations to multiple niches can yield important insights into ecosystem function and the microbiome's response to global change. However, microbial populations have remained elusive to the scientific community due to the challenges associated with isolating microorganisms in the laboratory. Today, advancements in large-scale metagenomics and metatranscriptomics facilitate the investigation of populations from many uncultured microbial species directly from their habitats. The knowledge acquired thus far reveals substantial genetic diversity among various microbial species, showcasing distinct patterns of population differentiation and adaptations, and highlighting the significant role of selection in structuring populations. In the coming years, population genomics is expected to significantly increase our understanding of the architecture and functioning of the ocean microbiome, providing insights into its vulnerability or resilience in the face of ongoing global change. Video Abstract.

Interplay Between Antimicrobial Resistance and Global Environmental Change

Antibiotic resistance genes predate the therapeutic uses of antibiotics. However, the current antimicrobial resistance crisis stems from our extensive use of antibiotics and the generation of environmental stressors that impose new selective pressure on microbes and drive the evolution of resistant pathogens that now threaten human health. Similar to climate change, this global threat results from human activities that change habitats and natural microbiomes, which in turn interact with human-associated ecosystems and lead to adverse impacts on human health. Human activities that alter our planet at global scales exacerbate the current resistance crisis and exemplify our central role in large-scale changes in which we are both protagonists and architects of our success but also casualties of unanticipated collateral outcomes. As cognizant participants in this ongoing planetary experiment, we are driven to understand and find strategies to curb the ongoing crises of resistance and climate change.

Character variation of root space microbial community composition in the response of drought-tolerant spring wheat to drought stress

Drought is the most prevalent environmental stress in crop production, posing a significant danger to food security. Microorganisms in the crop root zone affect crop growth and development, enhance effective nutrient use, and resist adversity hazards. To analyze the changes and functional differences of root space microbial (endosphere-rhizosphere-bulk soil) communities in spring wheat under drought stress. In this study, the root, rhizosphere, and bulk soil of the drought-tolerant group (DTG, three varieties) and drought-sensitive group (DSG, three varieties) were collected. The control (CK, 25-28%), moderate drought (MD, 15-18%), and severe drought (SD, 9-12%) were analyzed by high-throughput sequencing and bioinformatics. The results showed significant differences in the diversity of Bacteria and Fungi in the root space of spring wheat under drought stress (P < 0.05), with the drought-tolerant group exhibiting higher microbial diversity. The microbial community change in spring wheat root space was mainly determined by the niche differentiation of endosphere, rhizosphere, and bulk soil and declined from endosphere to bulk soil due to drought. The antagonism between microbial and root-space species increased, and the community's complexity and stability deteriorated. Enriching drought-resistant preference groups like Actinobaciota, Variovorax, Streptomyces, and Conocybe altered the structure and function of the microbial community in the root space of spring wheat. Spring wheat's root space Bacteria and Fungi have different strategies to respond to drought.

The divergent vertical pattern and assembly of soil bacterial and fungal communities in response to short-term warming in an alpine peatland

Soil microbial communities are crucial in ecosystem-level decomposition and nutrient cycling processes and are sensitive to climate change in peatlands. However, the response of the vertical distribution of microbial communities to warming remains unclear in the alpine peatland. In this study, we examined the effects of warming on the vertical pattern and assembly of soil bacterial and fungal communities across three soil layers (0-10, 10-20, and 20-30 cm) in the Zoige alpine peatland under a warming treatment. Our results showed that short-term warming had no significant effects on the alpha diversity of either the bacterial or the fungal community. Although the bacterial community in the lower layers became more similar as soil temperature increased, the difference in the vertical structure of the bacterial community among different treatments was not significant. In contrast, the vertical structure of the fungal community was significantly affected by warming. The main ecological process driving the vertical assembly of the bacterial community was the niche-based process in all treatments, while soil carbon and nutrients were the main driving factors. The vertical structure of the fungal community was driven by a dispersal-based process in control plots, while the niche and dispersal processes jointly regulated the fungal communities in the warming plots. Plant biomass was significantly related to the vertical structure of the fungal community under the warming treatments. The variation in pH was significantly correlated with the assembly of the bacterial community, while soil water content, microbial biomass carbon/microbial biomass phosphorous (MBC/MBP), and microbial biomass nitrogen/ microbial biomass phosphorous (MBN/MBP) were significantly correlated with the assembly of the fungal community. These results indicate that the vertical structure and assembly of the soil bacterial and fungal communities responded differently to warming and could provide a potential mechanism of microbial community assembly in the alpine peatland in response to warming.

Appetite Suppression and Interleukin 17 Receptor Signaling Activation of Colonic Mycobiota Dysbiosis Induced by High Temperature and High Humidity Conditions

It is known that the microbiome affects human physiology, emotion, disease, growth, and development. Most humans exhibit reduced appetites under high temperature and high humidity (HTHH) conditions, and HTHH environments favor fungal growth. Therefore, we hypothesized that the colonic mycobiota may affect the host’s appetite under HTHH conditions. Changes in humidity are also associated with autoimmune diseases. In the current study mice were fed in an HTHH environment (32°C ± 2°C, relative humidity 95%) maintained via an artificial climate box for 8 hours per day for 21 days. Food intake, the colonic fungal microbiome, the feces metabolome, and appetite regulators were monitored. Components of the interleukin 17 pathway were also examined. In the experimental groups food intake and body weight were reduced, and the colonic mycobiota and fecal metabolome were substantially altered compared to control groups maintained at 25°C ± 2°C and relative humidity 65%. The appetite-related proteins LEPT and POMC were upregulated in the hypothalamus (p < 0.05), and NYP gene expression was downregulated (p < 0.05). The expression levels of PYY and O-linked β-N-acetylglucosamine were altered in colonic tissues (p < 0.05), and interleukin 17 expression was upregulated in the colon. There was a strong correlation between colonic fungus and sugar metabolism. In fimo some metabolites of cholesterol, tromethamine, and cadaverine were significantly increased. There was significant elevation of the characteristic fungi Solicoccozyma aeria, and associated appetite suppression and interleukin 17 receptor signaling activation in some susceptible hosts, and disturbance of gut bacteria and fungi. The results indicate that the gut mycobiota plays an important role in the hypothalamus endocrine system with respect to appetite regulation via the gut-brain axis, and also plays an indispensable role in the stability of the gut microbiome and immunity. The mechanisms involved in these associations require extensive further studies.

Predicting spatial patterns of soil bacteria under current and future environmental conditions

Soil bacteria are largely missing from future biodiversity assessments hindering comprehensive forecasts of ecosystem changes. Soil bacterial communities are expected to be more strongly driven by pH and less by other edaphic and climatic factors. Thus, alkalinisation or acidification along with climate change may influence soil bacteria, with subsequent influences for example on nutrient cycling and vegetation. Future forecasts of soil bacteria are therefore needed. We applied species distribution modelling (SDM) to quantify the roles of environmental factors in governing spatial abundance distribution of soil bacterial OTUs and to predict how future changes in these factors may change bacterial communities in a temperate mountain area. Models indicated that factors related to soil (especially pH), climate and/or topography explain and predict part of the abundance distribution of most OTUs. This supports the expectations that microorganisms have specific environmental requirements (i.e., niches/envelopes) and that they should accordingly respond to environmental changes. Our predictions indicate a stronger role of pH over other predictors (e.g. climate) in governing distributions of bacteria, yet the predicted future changes in bacteria communities are smaller than their current variation across space. The extent of bacterial community change predictions varies as a function of elevation, but in general, deviations from neutral soil pH are expected to decrease abundances and diversity of bacteria. Our findings highlight the need to account for edaphic changes, along with climate changes, in future forecasts of soil bacteria.

Predicting microbiomes through a deep latent space

Motivation

Microbial communities influence their environment by modifying the availability of compounds, such as nutrients or chemical elicitors. Knowing the microbial composition of a site is therefore relevant to improve productivity or health. However, sequencing facilities are not always available, or may be prohibitively expensive in some cases. Thus, it would be desirable to computationally predict the microbial composition from more accessible, easily-measured features.

Results

Integrating deep learning techniques with microbiome data, we propose an artificial neural network architecture based on heterogeneous autoencoders to condense the long vector of microbial abundance values into a deep latent space representation. Then, we design a model to predict the deep latent space and, consequently, to predict the complete microbial composition using environmental features as input. The performance of our system is examined using the rhizosphere microbiome of Maize. We reconstruct the microbial composition (717 taxa) from the deep latent space (10 values) with high fidelity (>0.9 Pearson correlation). We then successfully predict microbial composition from environmental variables, such as plant age, temperature or precipitation (0.73 Pearson correlation, 0.42 Bray–Curtis). We extend this to predict microbiome composition under hypothetical scenarios, such as future climate change conditions. Finally, via transfer learning, we predict microbial composition in a distinct scenario with only 100 sequences, and distinct environmental features. We propose that our deep latent space may assist microbiome-engineering strategies when technical or financial resources are limited, through predicting current or future microbiome compositions.

Availability and implementation

Software, results and data are available at https://github.com/jorgemf/DeepLatentMicrobiome

Supplementary information

Supplementary data are available at Bioinformatics online.

Long-term stability of soil bacterial and fungal community structures revealed in their abundant and rare fractions

Despite the importance of soil microorganisms for ecosystem services, long‐term surveys of their communities are largely missing. Using metabarcoding, we assessed temporal dynamics of soil bacterial and fungal communities in three land‐use types, i.e., arable land, permanent grassland, and forest, over five years. Soil microbial communities remained relatively stable and differences over time were smaller than those among sites. Temporal variability was highest in arable soils. Indications for consistent shifts in community structure over five years were only detected at one site for bacteria and at two sites for fungi, which provided further support for long‐term stability of soil microbial communities. A sliding window analysis was applied to assess the effect of OTU abundance on community structures. Partial communities with decreasing OTU abundances revealed a gradually decreasing structural similarity with entire communities. This contrasted with the steep decline of OTU abundances, as subsets of rare OTUs (<0.01%) revealed correlations of up to 0.97 and 0.81 with the entire bacterial and fungal communities. Finally, 23.4% of bacterial and 19.8% of fungal OTUs were identified as scarce, i.e., neither belonging to site‐cores nor correlating to environmental factors, while 67.3% of bacterial and 64.9% of fungal OTUs were identified as rare but not scarce. Our results demonstrate high stability of soil microbial communities in their abundant and rare fractions over five years. This provides a step towards defining site‐specific normal operating ranges of soil microbial communities, which is a prerequisite for detecting community shifts that may occur due to changing environmental conditions or anthropogenic activities.

Diversity of Dominant Soil Bacteria Increases with Warming Velocity at the Global Scale

Understanding global soil bacterial diversity is important because of its role in maintaining a healthy global ecosystem. Given the effects of environmental changes (e.g., warming and human impact) on the diversity of animals and plants, effects on soil bacterial diversity are expected; however, they have been poorly evaluated at the global scale to date. Thus, in this study, we focused on the dominant soil bacteria, which are likely critical drivers of key soil processes worldwide, and investigated the effects of warming velocity and human activities on their diversity. Using a global dataset of bacteria, we performed spatial analysis to evaluate the effects of warming velocity and human activities, while statistically controlling for the potentially confounding effects of current climate and geographic parameters with global climate and geographic data. We demonstrated that the diversity of the dominant soil bacteria was influenced globally, not only by the aridity index (dryness) and pH but also by warming velocity from the Last Glacial Maximum (21,000 years ago) to the present, showing significant increases. The increase in bacterial diversity with warming velocity was particularly significant in forests and grasslands. An effect of human activity was also observed, but it was secondary to warming velocity. These findings provide robust evidence and advance our understanding of the effects of environmental changes (particularly global warming) on soil bacterial diversity at the global scale.

Soil properties and root traits jointly shape fine-scale spatial patterns of bacterial community and metabolic functions within a Korean pine forest

Spatial heterogeneity of soil bacterial community depends on scales. The fine-scale spatial heterogeneity of bacterial community composition and functions remains unknown. We analyzed the main driving factors of fine-scale spatial patterns of soil bacterial community composition and carbon metabolic functions across a 30 m × 40 m plot within a Korean pine forest by combining Illumina 16S rRNA sequencing with Biolog Ecoplates based on 53 soil samples. Clear spatial patterns in bacterial community composition and metabolic functions were observed in the forest soil. The bacterial community composition and metabolic functions both showed distance-decay of similarity within a distance of meters. Structural equation model analysis revealed that environmental variables and geographic distance together explained 37.9% and 63.1% of community and metabolic functions, respectively. Among all environmental factors, soil organic carbon (SOC) and root biomass emerged as the most important drivers of the bacterial community structure. In contrast, soil pH explained the largest variance in metabolic functions. Root biomass explained the second-largest variance in soil bacterial community composition, but root traits made no difference in metabolic functions variance. These results allow us to better understand the mechanisms controlling belowground diversity and plant-microbe interactions in forest ecosystems.

The spatial variation of soil bacterial community assembly processes affects the accuracy of source tracking in ten major Chinese cities

Urban soils harbor billions of bacterial cells and millions of species. However, the distribution patterns and assembly processes of bacterial communities remain largely uncharacterized in urban soils. It is also unknown if we can use the bacteria to track soil sources to certain cities and districts. Here, Illumina MiSeq sequencing was used to survey soil bacterial communities from 529 random plots spanning 61 districts and 10 major cities in China. Over a 3,000 km range, community similarity declined with increasing geographic distance (Mantel r=0.62), and community composition was clustered by city (R²=0.50). Within cities (<100 km), the aforementioned biogeographic patterns were weakened. Process analysis showed that homogenizing dispersal and dispersal limitation dominated soil bacterial assembly at small and large spatial scales, respectively. Accordingly, the probabilities of accurately tracking random soil sources to certain cities and districts were 90.0% and 66.7%, respectively. When the tested samples originated from cities that were more than 1,265 km apart, the soil sources could be identified with nearly 100% accuracy. Overall, this study demonstrates the strong distance-decay relationship and the clear geographic zoning of urban soil bacterial communities among cities. The varied importance of different community assembly processes at multiple spatial scales strongly affects the accuracy of microbial source tracking.

Compounding Effects of Climate Warming and Antibiotic Resistance

Bacteria have evolved diverse mechanisms to survive environments with antibiotics. Temperature is both a key factor that affects the survival of bacteria in the presence of antibiotics and an environmental trait that is drastically increasing due to climate change. Therefore, it is timely and important to understand links between temperature changes and selection of antibiotic resistance. This review examines these links by synthesizing results from laboratories, hospitals, and environmental studies. First, we describe the transient physiological responses to temperature that alter cellular behavior and lead to antibiotic tolerance and persistence. Second, we focus on the link between thermal stress and the evolution and maintenance of antibiotic resistance mutations. Finally, we explore how local and global changes in temperature are associated with increases in antibiotic resistance and its spread. We suggest that a multidisciplinary, multiscale approach is critical to fully understand how temperature changes are contributing to the antibiotic crisis.

Soil Microbial Biogeography in a Changing World: Recent Advances and Future Perspectives

Soil microbial communities are fundamental to maintaining key soil processes associated with litter decomposition, nutrient cycling, and plant productivity and are thus integral to human well-being. Recent technological advances have exponentially increased our knowledge concerning the global ecological distributions of microbial communities across space and time and have provided evidence for their contribution to ecosystem functions. However, major knowledge gaps in soil biogeography remain to be addressed over the coming years as technology and research questions continue to evolve. In this minireview, we state recent advances and future directions in the study of soil microbial biogeography and discuss the need for a clearer concept of microbial species, projections of soil microbial distributions toward future global change scenarios, and the importance of embracing culture and isolation approaches to determine microbial functional profiles. This knowledge will be critical to better predict ecosystem functions in a changing world.

Interannual climate variability and altered precipitation influence the soil microbial community structure in a Tibetan Plateau grassland

Climate change could influence aboveground and belowground plant community diversity and structure profoundly. However, our understanding of the responses of microbial communities to changes in both temperature and precipitation remains poor. Here, using 16S rDNA and ITS high throughput sequencing, we investigated the responses of soil bacterial and fungal community structure to both temperature and precipitation changes, and how such changes could influence interannual variability within soil microbial communities in a grassland in the Tibetan Plateau. The altered precipitation treatments had significant effects on soil bacterial and fungal community structure (F = 2.11, P = 0,001; F = 2.26. P = 0.001, respectively), while year had a more significant effect on soil bacterial and fungal community structure (F = 3.36, P = 0.001; F = 2.67, P = 0.001, respectively). The results showed that the interannual fluctuations in mean annual precipitation and mean annual temperature were significantly correlated with the interannual variations in soil bacterial and fungal community structures. In addition, the robustness of co-occurrence relationships among microbes could be strongly influenced by the altered precipitation and year. Overall, our results indicated that the effect of interannual climate variability on the soil microbial community was greater than the effect of a 1.6 °C increase in temperature. Our findings suggest an interactive effect of rapid interannual variability and slow climate change on the belowground soil microbial community structure.

Current State of and Future Opportunities for Prediction in Microbiome Research: Report from the Mid-Atlantic Microbiome Meet-up in Baltimore on 9 January 2019

Accurate predictions across multiple fields of microbiome research have far-reaching benefits to society, but there are few widely accepted quantitative tools to make accurate predictions about microbial communities and their functions. More discussion is needed about the current state of microbiome analysis and the tools required to overcome the hurdles preventing development and implementation of predictive analyses. We summarize the ideas generated by participants of the Mid-Atlantic Microbiome Meet-up in January 2019. While it was clear from the presentations that most fields have advanced beyond simple associative and descriptive analyses, most fields lack essential elements needed for the development and application of accurate microbiome predictions. Participants stressed the need for standardization, reproducibility, and accessibility of quantitative tools as key to advancing predictions in microbiome analysis. We highlight hurdles that participants identified and propose directions for future efforts that will advance the use of prediction in microbiome research.

Soil microbes that may accompany climate warming increase alpine plant production

Climate change is causing species with non-overlapping ranges to come in contact, and a key challenge is to predict the consequences of such species re-shuffling. Experiments on plants have focused largely on novel competitive interactions; other species interactions, such as plant-microbe symbioses, while less studied, may also influence plant responses to climate change. In this greenhouse study, we evaluated interactions between soil microbes and alpine-restricted plant species, simulating a warming scenario in which low-elevation microbes migrate upslope into the distribution of alpine plants. We examined three alpine grasses from the Rocky Mountains, CO, USA (Poa alpina, Festuca brachyphylla, and Elymus scribneri). We used soil inocula from within (resident) or below (novel) the plants' current elevation range and examined responses in plant biomass, plant traits, and fungal colonization of roots. Resident soil inocula from the species' home range decreased biomass to a greater extent than novel soil inocula. The depressed growth in resident soils suggested that these soils harbor more carbon-demanding microbes, as plant biomass generally declined with greater fungal colonization of roots, especially in resident soil inocula. Although plant traits did not respond to the provenance of soil inocula, specific leaf area declined and root:shoot ratio increased when soil inocula were sterilized, indicating microbial mediation of plant trait expression. Contrary to current predictions, our findings suggest that if upwardly migrating microbes were to displace current soil microbes, alpine plants may benefit from this warming-induced microbial re-shuffling.

Factors influencing aquatic and terrestrial bacterial community assembly

During recent years, many studies have shown that different processes including drift, environmental selection and dispersal can be important for the assembly of bacterial communities in aquatic and terrestrial ecosystems. However, we lack a conceptual overview about the ecological context and factors that influence the relative importance of the different assembly mechanisms and determine their dynamics in time and space. Focusing on free-living, i.e., nonhost associated, bacterial communities, this minireview, therefore, summarizes and conceptualizes findings from empirical studies about how (i) environmental factors, such as environmental heterogeneity, disturbances, productivity and trophic interactions; (ii) connectivity and dispersal rates (iii) spatial scale, (iv) community properties and traits and (v) the use of taxonomic/phylogenetic or functional metrics influence the relative importance of different community assembly processes. We find that there is to-date little consistency among studies and suggest that future studies should now address how (i)-(v) differ between habitats and organisms and how this, in turn, influences the temporal and spatial-scale dependency of community assembly processes in microorganisms.

Spatial, Temporal, and Phylogenetic Scales of Microbial Ecology

Microbial communities play a major role in disease, biogeochemical cycling, agriculture, and bioremediation. However, identifying the ecological processes that govern microbial community assembly and disentangling the relative impacts of those processes has proven challenging. Here, we propose that this discord is due to microbial systems being studied at different spatial, temporal, and phylogenetic scales. We argue that different processes dominate at different scales, and that through a more explicit consideration of spatial, temporal, and phylogenetic grains and extents (the two components of scale) a more accurate, clear, and useful understanding of microbial community assembly can be developed. We demonstrate the value of applying ecological concepts of scale to microbiology, specifically examining their application to nestedness, legacy effects, and taxa-area relationships of microbial systems. These proposed considerations of scale will help resolve long-standing debates in microbial ecology regarding the processes determining the assembly of microbial communities, and provide organizing principles around which hypotheses and theories can be developed.

Uncovering the Uncultivated Majority in Antarctic Soils: Toward a Synergistic Approach

Although Antarctica was once believed to be a sterile environment, it is now clear that the microbial communities inhabiting the Antarctic continent are surprisingly diverse. Until the beginning of the new millennium, little was known about the most abundant inhabitants of the continent: prokaryotes. From then on, however, the rising use of deep sequencing techniques has led to a better understanding of the Antarctic prokaryote diversity and provided insights in the composition of prokaryotic communities in different Antarctic environments. Although these cultivation-independent approaches can produce millions of sequences, linking these data to organisms is hindered by several problems. The largest difficulty is the lack of biological information on large parts of the microbial tree of life, arising from the fact that most microbial diversity on Earth has never been characterized in laboratory cultures. These unknown prokaryotes, also known as microbial dark matter, have been dominantly detected in all major environments on our planet. Laboratory cultures provide access to the complete genome and the means to experimentally verify genomic predictions and metabolic functions and to provide evidence of horizontal gene transfer. Without such well-documented reference data, microbial dark matter will remain a major blind spot in deep sequencing studies. Here, we review our current understanding of prokaryotic communities in Antarctic ice-free soils based on cultivation-dependent and cultivation-independent approaches. We discuss advantages and disadvantages of both approaches and how these strategies may be combined synergistically to strengthen each other and allow a more profound understanding of prokaryotic life on the frozen continent.