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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

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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

Protist taxonomy in context The increasing availability over the past two decades of gene sequence data for protists has fired an energetic and rapidly moving field of taxonomic development and debate, in response to many exciting and often very surprising findings. The classic subdivisions of microbial eukaryotes into four main groups – amoeboid organisms, flagellates, ciliates and sporozoa (a group of parasites) – formulated in the 19th century and current throughout a large part of the 20th appeals because of its simplicity, but almost could not be more wrong. The history of protist taxonomy is not the subject of this chapter, but a diversity of perspectives can be found in (among others) Adl et al. (2005; 2007; 2012), Cavalier-Smith (1998), Corliss (1984), Levine et al. (1980), Walker et al. (2011) and references therein. There are several characteristics of protists that have contributed to this taxonomic turbulence. Their size makes detailed observation non-trivial; individual approaches, skills and tools applied to morphological taxonomic studies have varied significantly over time, and continue to do so. Their single-celled and/or non-differentiated forms do not offer many easily observable characters for either the taxonomist or natural selection to work on. A consequence of the latter is extremely high levels of convergent evolution at different evolutionary scales. Some very striking examples of convergence have been revealed by molecular phylogenetic analyses, which demonstrate the extent to which the pre-molecular subdivision of protists was incorrect (e.g. Nikolaev et al. 2004; Richards and Talbot 2007; Richards et al. 2011; S. D. Brown et al. 2012). Some other important factors contributing to taxonomic difficulties are (1) the unknown sexual status of most protists and therefore the inapplicability and/or uncertainty of applying the biological species concept (sex is known for some but many are presumed asexual at least in the mid to long term), (2) highly incomplete and patchy knowledge of the diversity of many protist groups and regions of the eukaryote Tree of Life in which knowledge of lineage diversity and biology is generally poor, (3) the absence of a generally agreed or applicable species concept for most protist groups, and (4) difficulty of culturing many lineages.

Protist systematics, ecology and next generation sequencing

There has been limited characterisation of bat-borne coronaviruses in Europe. Here, we screened for coronaviruses in 48 faecal samples from 16 of the 17 bat species breeding in the UK, collected through a bat rehabilitation and conservationist network. We recovered nine (two novel) complete genomes across six bat species: four alphacoronaviruses, a MERS-related betacoronavirus, and four closely related sarbecoviruses. We demonstrate that at least one of these sarbecoviruses can bind and use the human ACE2 receptor for infecting human cells, albeit suboptimally. Additionally, the spike proteins of these sarbecoviruses possess an R-A-K-Q motif, which lies only one nucleotide mutation away from a furin cleavage site (FCS) that enhances infectivity in other coronaviruses, including SARS-CoV-2. However, mutating this motif to an FCS does not enable spike cleavage. Overall, while UK sarbecoviruses would require further molecular adaptations to infect humans, their zoonotic risk is unknown and warrants closer surveillance.

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Genomic screening of 16 UK native bat species through conservationist networks uncovers coronaviruses with zoonotic potential

Exposure to pharmaceutical pollution originating from sewage effluent is an unavoidable component of freshwater microbial life Despite this ‘home truth’, the extent to which these pollutants influence the composition and function of freshwater microbial systems remains unclear Tamiflu is an antiviral with unprecedented projected use patterns during an influenza pandemic (Singer et al 2008; Singer et al 2011) The impact this pulse of bioactive drug will have on the resilience of freshwater microbial communities remains unexplored

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How immigration might alleviate the effects of an influenza pandemic: a freshwater microbiology story

Open freshwater systems show some resilience to the impact of sewage effluent on a species level.
Even in systems in which changes to the microbial system are masked by bacterial seeding from
upstream, the impact of sewage can be shown by a higher prevalence and abundance of class I
integrons. This change, which brings about greater antibiotic resistance – and all the problems this
entails - should not be ignored. Heavily sewage impacted rivers like the Kennet might have a microbial
system that has already adjusted to continuous heightened SE input.

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Dynamics of freshwater microbial communities in two different rivers exposed to sewage effluent in novel in situ mesocosms

Understanding the temperature dependence of carbon use efficiency (CUE) is critical for understanding microbial physiology, population dynamics, and community-level responses to changing environmental temperatures 1,2. Currently, microbial CUE is widely assumed to decrease with temperature 3,4. However, this assumption is based largely on community-level data, which are influenced by many confounding factors 5, with little empirical evidence at the level of individual strains. Here, we experimentally characterise the CUE thermal response for a diverse set of environmental bacterial isolates. We find that contrary to current thinking, bacterial CUE typically responds either positively to temperature, or has no discernible temperature response, within biologically meaningful temperature ranges. Using a global data-synthesis, we show that our empirical results are generalisable across a much wider diversity of bacteria than have previously been tested. This systematic variation in the thermal responses of bacterial CUE 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 fundamental new insights into microbial physiology, and a basis for more accurately modelling the effects of shorter-term thermal fluctuations as well as longer-term climatic warming on microbial communities.

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Thomas Bell

Papers

Protist systematics, ecology and next generation sequencing

Genomic screening of 16 UK native bat species through conservationist networks uncovers coronaviruses with zoonotic potential

How immigration might alleviate the effects of an influenza pandemic: a freshwater microbiology story

Dynamics of freshwater microbial communities in two different rivers exposed to sewage effluent in novel in situ mesocosms

Systematic variation in the temperature dependence of bacterial carbon use efficiency