Fifty important research questions in microbial ecology

Antwis, Rachael E.; Griffiths, Sarah M.; Harrison, Xavier A.; Aranega-Bou, Paz; Arce, Andres N.; Bettridge, Aimee S.; Brailsford, Francesca L.; Menezes, Alexandre B. de; Devaynes, Andrew; Forbes, Kristian M.; Fry, Ellen L.; Goodhead, Ian; Haskell, Erin; Heys, Chloe; James, Chloë E.; Johnston, Sarah; Lewis, Gillian; Lewis, Zenobia; Macey, Michael C.; McCarthy, Alan J.; McDonald, James E.; Mejia-Florez, Nasmille L.; O’Brien, David; Orland, Chloé; Pautasso, Marco; Reid, William D.; Robinson, Heather A.; Wilson, Kenneth; Sutherland, William J.

doi:10.1093/femsec/fix044

Cited by 171 publications

(123 citation statements)

References 78 publications

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“…'N' indicates that there were no functional data for this microbe. See Figure S6 for the OTU correlation matrix with names included microbial communities, beyond the population scale, is a major challenge for microbial ecology (Antwis et al, 2017;Camp, Kanther, Semova, & Rawls, 2009). Based on our findings, we suggest that larger geographical and/or temporal scales are needed to detect possible impacts of host characteristics on the structure of gut microbial communities.…”

Section: Discussionmentioning

confidence: 99%

Microbial associations and spatial proximity predict North American moose (Alces alces) gastrointestinal community composition

Fountain-Jones

Clark

Kinsley

et al. 2020

Journal of Animal Ecology

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Microbial communities are increasingly recognized as crucial for animal health. However, our understanding of how microbial communities are structured across wildlife populations is poor. Mechanisms such as interspecific associations are important in structuring free‐living communities, but we still lack an understanding of how important interspecific associations are in structuring gut microbial communities in comparison with other factors such as host characteristics or spatial proximity of hosts. Here, we ask how gut microbial communities are structured in a population of North American moose Alces alces. We identify key microbial interspecific associations within the moose gut and quantify how important they are relative to key host characteristics, such as body condition, for predicting microbial community composition. We sampled gut microbial communities from 55 moose in a population experiencing decline due to a myriad of factors, including pathogens and malnutrition. We examined microbial community dynamics in this population utilizing novel graphical network models that can explicitly incorporate spatial information. We found that interspecific associations were the most important mechanism structuring gut microbial communities in moose and detected both positive and negative associations. Models only accounting for associations between microbes had higher predictive value compared to models including moose sex, evidence of previous pathogen exposure or body condition. Adding spatial information on moose location further strengthened our model and allowed us to predict microbe occurrences with ~90% accuracy. Collectively, our results suggest that microbial interspecific associations coupled with host spatial proximity are vital in shaping gut microbial communities in a large herbivore. In this case, previous pathogen exposure and moose body condition were not as important in predicting gut microbial community composition. The approach applied here can be used to quantify interspecific associations and gain a more nuanced understanding of the spatial and host factors shaping microbial communities in non‐model hosts.

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Section: Discussionmentioning

confidence: 99%

Microbial associations and spatial proximity predict North American moose (Alces alces) gastrointestinal community composition

Fountain-Jones

Clark

Kinsley

et al. 2020

Journal of Animal Ecology

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“…Host–microbiome systems are complex ecological communities encompassing an array of host–microbe and microbe–microbe interactions (Bauer, Kainz, Carmona‐Gutierrez, & Madeo, ; Coyte, Schluter, & Foster, ). Understanding the ecological and evolutionary nature of the relationship between hosts and their microbiome requires an understanding of the forces structuring these microbial communities, driven by both host and environment (Antwis et al, ).…”

Section: Introductionmentioning

confidence: 99%

Host genetics and geography influence microbiome composition in the spongeIrcinia campana

Griffiths

Antwis

Lenzi

et al. 2019

Journal of Animal Ecology

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Marine sponges are hosts to large, diverse communities of microorganisms. These microbiomes are distinct among sponge species and from seawater bacterial communities, indicating a key role of host identity in shaping its resident microbial community. However, the factors governing intraspecific microbiome variability are underexplored and may shed light on the evolutionary and ecological relationships between host and microbiome.Here, we examined the influence of genetic variation and geographic location on the composition of the Ircinia campana microbiome.We developed new microsatellite markers to genotype I. campana from two locations in the Florida Keys, USA, and characterized their microbiomes using V4 16S rRNA amplicon sequencing.We show that microbial community composition and diversity is influenced by host genotype, with more genetically similar sponges hosting more similar microbial communities. We also found that although I. campana was not genetically differentiated between sites, microbiome composition differed by location.Our results demonstrate that both host genetics and geography influence the composition of the sponge microbiome. Host genotypic influence on microbiome composition may be due to stable vertical transmission of the microbial community from parent to offspring, making microbiomes more similar by descent. Alternatively, sponge genotypic variation may reflect variation in functional traits that influence the acquisition of environmental microbes. This study reveals drivers of microbiome variation within and among locations, and shows the importance of intraspecific variability in mediating eco‐evolutionary dynamics of host‐associated microbiomes.

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“…Understanding the structure and function of communities is a central theme in ecology. This is particularly difficult to study in microbial communities because the species concept is difficult to apply and because the communities are highly dynamic (Antwis et al, ). Already a common approach in plant and animal ecology, trait‐based ecological research is starting to gain traction in microbial ecology as a way to assess the biogeography of microbial communities and overcome the constraint of species diversity and ambiguity (Crowther et al, ; Green, Bohannan, & Whitaker, ).…”

Section: Introductionmentioning

confidence: 99%

A meta‐analysis of temperature sensitivity as a microbial trait

Alster

Weller

Fischer

2018

Global Change Biology

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Traits-based approaches in microbial ecology provide a valuable way to abstract organismal interaction with the environment and to generate hypotheses about community function. Using macromolecular rate theory (MMRT), we recently identified that temperature sensitivity can be characterized as a distinct microbial trait. As temperature is fundamental in controlling biological reactions, variation in temperature sensitivity across communities, organisms, and processes has the potential to vastly improve understanding of microbial response to climate change. These microbial temperature sensitivity traits include the heat capacity (ΔCP‡), temperature optimum (T ), and point of maximum temperature sensitivity (TS ), each of which provide unique insights about organismal response to changes in temperature. In this meta-analysis, we analyzed the distribution of these temperature sensitivity traits from bacteria, fungi, and mixed communities across a variety of biological systems (e.g., soils, oceans, foods, wastewater treatment plants) in order to identify commonalities in temperature responses across these diverse organisms and reaction rates. Our analysis of temperature sensitivity traits from over 350 temperature response curves reveals a wide distribution of temperature sensitivity traits, with T and TS well within biological relevant temperatures. We find that traits vary significantly depending on organism type, microbial diversity, source environment, and biological process, with higher temperature sensitivity found in fungi than bacteria and in less diverse systems. Carbon dioxide production was found to be less temperature sensitive than denitrification, suggesting that changes in temperature will have a potentially larger impact on nitrogen-related processes. As climate changes, these results have important implications for basic understanding of the temperature sensitivity of biological reactions and for ecological understanding of species' trait distributions, as well as for improved treatment of temperature sensitivity in models.

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Fifty important research questions in microbial ecology

Cited by 171 publications

References 78 publications

Microbial associations and spatial proximity predict North American moose (Alces alces) gastrointestinal community composition

Microbial associations and spatial proximity predict North American moose (Alces alces) gastrointestinal community composition

Host genetics and geography influence microbiome composition in the spongeIrcinia campana

A meta‐analysis of temperature sensitivity as a microbial trait

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