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Microbes are the unseen majority in soil and comprise a large portion of lifes genetic diversity. Despite their abundance, the impact of soil microbes on ecosystem processes is still poorly understood. Here we explore the various roles that soil microbes play in terrestrial ecosystems with special emphasis on their contribution to plant productivity and diversity. Soil microbes are important regulators of plant productivity, especially in nutrient poor ecosystems where plant symbionts are responsible for the acquisition of limiting nutrients. Mycorrhizal fungi and nitrogenfixing bacteria are responsible for c. 5‐20% (grassland and savannah) to 80% (temperate and boreal forests) of all nitrogen, and up to 75% of phosphorus, that is acquired by plants annually. Free-living microbes also strongly regulate plant productivity, through the mineralization of, and competition for, nutrients that sustain plant productivity. Soil microbes, including microbial pathogens, are also important regulators of plant community dynamics and plant diversity, determining plant abundance and, in some cases, facilitating invasion by exotic plants. Conservative estimates suggest that c. 20 000 plant species are completely dependent on microbial symbionts for growth and survival pointing to the importance of soil microbes as regulators of plant species richness on Earth. Overall, this review shows that soil microbes must be considered as important drivers of plant diversity and productivity in terrestrial ecosystems.

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The unseen majority: Soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems

Bacterial biofilms are formed by communities that are embedded in a self-produced matrix of extracellular polymeric substances (EPS). Importantly, bacteria in biofilms exhibit a set of 'emergent properties' that differ substantially from free-living bacterial cells. In this Review, we consider the fundamental role of the biofilm matrix in establishing the emergent properties of biofilms, describing how the characteristic features of biofilms - such as social cooperation, resource capture and enhanced survival of exposure to antimicrobials - all rely on the structural and functional properties of the matrix. Finally, we highlight the value of an ecological perspective in the study of the emergent properties of biofilms, which enables an appreciation of the ecological success of biofilms as habitat formers and, more generally, as a bacterial lifestyle.

Biofilms: an emergent form of bacterial life.

We review the biogeography of microorganisms in light of the biogeography of macroorganisms A large body of research supports the idea that free-living microbial taxa exhibit biogeographic patterns Current evidence confirms that, as proposed by the Baas-Becking hypothesis, 'the environment selects' and is, in part, responsible for spatial variation in microbial diversity However, recent studies also dispute the idea that 'everything is everywhere' We also consider how the processes that generate and maintain biogeographic patterns in macroorganisms could operate in the microbial world

/pdf/microbial-biogeography-putting-microorganisms-on-the-map-1k7e5do5pn.pdf

Microbial biogeography : putting microorganisms on the map

Metagenomics and 16S pyrosequencing have enabled the study of ecosystem structure and dynamics to great depth and accuracy. Co-occurrence and correlation patterns found in these data sets are increasingly used for the prediction of species interactions in environments ranging from the oceans to the human microbiome. In addition, parallelized co-culture assays and combinatorial labelling experiments allow high-throughput discovery of cooperative and competitive relationships between species. In this Review, we describe how these techniques are opening the way towards global ecosystem network prediction and the development of ecosystem-wide dynamic models.

Microbial interactions: from networks to models

Intraspecific negative feedback effects, where performance is reduced on soils conditioned by conspecifics, are widely documented in plant communities. However, interspecific feedbacks are less well studied, and their direction, strength, causes, and consequences are poorly understood. If more closely related species share pathogens, or have similar soil resource requirements, plants may perform better on soils conditioned by more distant phylogenetic relatives. There have been few empirical tests of this prediction across plant life stages, and none of which attempt to account for soil chemistry. Here, we test the utility of phylogeny for predicting soil feedback effects on plant survival and performance (germination, seedling survival, growth rate, biomass). We implement a full factorial experiment growing species representing five families on five plant family-specific soil sources. Our experiments exploit soils that have been cultured for over 30 years in plant family-specific beds at Oxford University Botanic Gardens. Plant responses to soil source were idiosyncratic, and species did not perform better on soils cultured by phylogenetically more distant relatives. The magnitude and sign of feedback effects could, however, be explained by differences in the chemical properties of “home” and “away” soils. Furthermore, the direction of soil chemistry-related plant-soil feedbacks was dependent on plant life stage, with the effects of soil chemistry on germination success and accumulation of biomass inversely related. Our results (1) suggest that the phylogenetic distance between plant families cannot predict plant–soil feedbacks across multiple life stages, and (2) highlight the need to consider changes in soil chemistry as an important driver of population responses. The contrasting responses at plant life stages suggest that studies focusing on brief phases in plant demography (e.g., germination success) may not give a full picture of plant–soil feedback effects.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.1487

Plant-soil feedbacks from 30-year family-specific soil cultures: phylogeny, soil chemistry and plant life stage.

Many roads to bacterial generalism.

Theory predicts that immigration can either enhance or impair the rate at which species and whole communities adapt to environmental change, depending on the traits of genotypes and species in the source pool relative to local conditions. These responses, in turn, will determine how well whole communities function in changing environments. We tested the effects of immigration and experimental warming on microbial communities during an 81-day field experiment. The effects of immigration depended on the warming treatment. In warmed communities, immigration was detrimental to community growth, whereas in ambient communities it was beneficial. This result is explained by colonists coming from a local species pool preadapted to ambient conditions. Loss of metabolic diversity, however, was buffered by immigration in both environments. Communities showed increasing local adaptation to temperature conditions during the experiment, and this was independent of whether they received immigration. Genotypes that comprised the communities were not locally adapted, however, indicating that community local adaptation can be independent of adaptation of component genotypes. Our results are consistent with a greater role for species interactions rather than adaptation of constituent species in determining local adaptation of whole communities and confirm that immigration can either enhance or impair community responses to environmental change depending on the environmental context.

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The Effect of Immigration on the Adaptation of Microbial Communities to Warming.

Hypotheses and predictions of the landscape-level impact of agriculture on soil microbial communities, and the consequences for ecosystem functioning in adjacent unmodified environments

Table S1: Summary of the hypotheses from Microbes in the Anthropocene: spillover of agriculturally selected bacteria and their impact on natural ecosystems

Carbon use efficiency (CUE) is a key characteristic of microbial physiology and underlies community-level responses to changing environments. Yet, we currently lack general empirical insights into variation in microbial CUE at the level of individual taxa. Here, through experiments with 29 strains of environmentally isolated bacteria, we find that bacterial CUE typically responds either positively to temperature, or has no discernible response, within biologically meaningful temperature ranges. Using a global data synthesis, we show that these results are generalisable across most culturable groups of bacteria. This variation in the thermal responses of bacterial CUE is taxonomically structured, and stems from the fact that relative to respiration rates, bacterial population growth rates typically respond more strongly to temperature, and are also subject to weaker evolutionary constraints. Our results provide new insights into microbial physiology, and a basis for more accurately modelling the effects of thermal fluctuations on complex microbial communities.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/ele.13840

Thomas Bell

Papers

Plant-soil feedbacks from 30-year family-specific soil cultures: phylogeny, soil chemistry and plant life stage.

Many roads to bacterial generalism.

The Effect of Immigration on the Adaptation of Microbial Communities to Warming.

Table S1: Summary of the hypotheses from Microbes in the Anthropocene: spillover of agriculturally selected bacteria and their impact on natural ecosystems

Systematic variation in the temperature dependence of bacterial carbon use efficiency.