Microbial Ecology

Understanding ecological interactions in microbial communities is limited by lack of informative longitudinal abundance data necessary for reliable inference. Here, Xiao et al. develop a method to infer the interactions between microbes based on their abundances in steady-state samples.

How a trait evolves depends on the shape of its fitness trade-off. Here, Huang et al. demonstrate evolution of trade-off shape in an experimental predator-prey system and develop a mathematical model of trait evolution when the underlying trade-off can also evolve.

Predatory or competitive interactions between microbes are poorly understood but likely influence global nutrient cycles. Here, the authors show that Pseudomonas bacteria could immobilize algal cells, potential prey, by releasing secondary metabolites that induce a Ca²⁺ signal and algal deflagellation.

Virophages are recently-identified small viruses that infect larger viruses, yet their diversity and ecological roles are poorly understood. Here, Roux and colleagues present time series metagenomics data revealing new virophage genera and their putative ecological interactions in two freshwater lakes.

Viruses are partners in ecosystem ecology, yet their study has been primarily limited to laboratory models virus-host or derived from metagenomics. Here, Moniruzzamanet al. use metatranscriptomics to resolve interactions between giant viruses and single-celled eukaryotic hosts.

Hosts vary in how dependent they are on their beneficial symbionts. Here, Fisher and colleagues analyse the results of symbiont-removal experiments from 106 symbioses in a phylogenetic context and show that host dependence is associated with symbiont transmission mode, function, and genome size.

Bacteria can exchange nutrients and macromolecules through tubular membranous structures called nanotubes. Here, the authors show that Bacillus subtilis can kill and prey on Bacillus megaterium by delivering a toxin and extracting nutrients in a nanotube-dependent manner.

The maintenance of bacterial and fungal activity is essential for ecosystem functioning, particularly in dry soils where the two phyla co-exist. Here, Worrich and colleagues show experimentally that mycelia traffic water and nutrients and thereby stimulate bacterial activity in stressful conditions.

Cells of the yeast Saccharomyces cerevisiaecan mate with other cells of opposite mating type. Here, the authors show that the combination of a pheromone and a pheromone-degrading enzyme allows yeast cells to monitor relative mate abundance within a population and adjust their commitment to sexual reproduction.

Network stability is a central topic in theoretical ecology, with most work focusing on mutualistic or food web networks. Here, the authors explore the stability of microbial networks based on the consumption and exchange of resources, showing that asymmetry in crossfeeding relationships can destabilize networks.

Higher-order interactions occur when one species mediates the interaction between two others. Here, the authors model microbial growth and competition to show that higher-order interactions can arise from tradeoffs in growth traits, leading to neutral coexistence and other complex dynamics.

We know little about the effect of relationships between species on the assembly of microbial communities. Here the authors map pairwise invasion relations between bacteria and find that instead of one strain dominating, inhibitory interactions mean that often neither strain can invade the other.

Particles of organic matter in the ocean harbour microbial communities that digest and recycle essential nutrients. Here, Datta et al.use model marine particles to show that the attached bacterial communities undergo rapid, reproducible successions driven by ecological interactions.

Microbes live in communities and exchange metabolites, but the resulting dynamics are poorly understood. Here, the authors study the interplay between metabolite production strategies and population dynamics, and find that complex and unexpected dynamics emerge even in simple microbial economies.

Cooperative behaviour among individuals provides a collective benefit, but is considered costly. Using Pseudomonas aeruginosa as a model system, the authors show that secretion of the siderophore pyoverdine only incurs a fitness cost and favours cheating when its building blocks carbon or nitrogen are growth-limiting.

Lab strains of Pseudomonas are model systems for the evolution of cooperation over public goods (iron-scavenging siderophores). Here, Butaitė et al. add ecological and evolutionary insight into this system by showing that cheating and resistance to cheating both shape competition for iron in natural Pseudomonas communities.

The rise of metabolic interdependencies among microbes is still poorly understood. Here, taking the underlying biochemical networks into consideration, Zomorrodi and Segrè integrate genome-scale metabolic models with evolutionary game theory to study the rise of cross-feeding in microbial communities.

Symbiotic microbial communities aid their hosts through developmental and environmental transitions. Here, the authors show that host morphological plasticity is associated with predictable changes in a phenotype-specific microbiome in three species of sea urchin larvae.

Drought conditions can alter the composition of soil microbial communities, but the effects of drought on network properties have not been tested. Here, de Vries and colleagues show that co-occurrence networks are destabilised under drought for bacteria but not fungi.

Whether marine microbes form strongly differentiated communities over time remains unknown. Here, Martin-Platero and colleagues develop a time series analysis to characterize marine bacteria and Eukarya communities at a fine temporal grain, revealing cohesive but rapidly changing communities.

Interactions with other microbes may inhibit or facilitate the dispersal of bacteria. Here, Zhang et al. use cheese rind microbiomes as a model to show that physical networks created by filamentous fungi can affect the dispersal of motile bacteria and thus shape the diversity of microbial communities.

Microbes adapting to broad and specialized ranges of environments (generalists and specialists) have distinct ecological roles and properties. Via meta-analysis of community sequencing datasets, Sriswasdi et al. show that generalists have higher speciation rates and persistence advantage over specialists.

Host-associated microbial communities can shift in structure or function when hosts change locations. Bletzet al. reciprocally transfer salamander larvae between pond and stream habitats to show that gut microbiomes shift in function, but not necessarily taxonomic identities, when hosts encounter a new environment.

Environmental factors often outweigh host heritable factors in structuring host-associated microbiomes. Here, Bowen et al. show that host lineage is crucial for determination of rhizosphere bacterial communities in Phragmites australis, a globally distributed invasive plant.

Both host diet and phylogeny have been argued to shape mammalian microbiome communities. Here, the authors show that diet predicts the presence of ancient bacterial lineages in the microbiome, but that co-speciation between more recent bacterial lineages and their hosts may drive associations between microbiome composition and phylogeny.

Though both the presence and traits of a species can influence the dynamics of its ecological community, the effects of these factors are difficult to disentangle. Here, Gómez et al. demonstrate in a microbial mesocosm that local adaptation of a focal species can influence the community as much as the presence of the focal species per se.

Particle-attached bacteria play a key ecosystem role by degrading complex organic materials in the ocean. Here, the authors use model marine microbial communities to show that community composition and interspecies interactions can significantly slowdown the rates of particle turnover in the environment.

Nitrite tends to peak at the base of the sunlit zone in the ocean, but the ecological drivers of the local and global distributions of nitrite are not known. Here, Zakem et al. use a marine ecosystem model to show how the interactions of nitrifying microbes mediate nitrite accumulation.

Convenient methods for assessing microbial community structure in terms of biomass are lacking. Here, the authors present a metaproteomics-based approach for assessing microbial community structure using protein abundance as a measure for biomass contributions of individual populations.

The role of ecosystem structure in microbial activity related to greenhouse gas production is poorly understood. Here, Taş and colleagues show that microbial communities and ecosystem function vary across fine-scale topography in a polygonal tundra.

The role of microbial communities in regime shifts is poorly understood. Here, the authors use a mathematical model and field data from a seasonally stratified lake to show that gradual environmental changes can induce oxic-anoxic regime shifts mediated by microbial community dynamics and redox processes.

Yeoh et al. study root microbiomes of different plant phyla across a tropical soil chronosequence. They confirm that soil type is the primary determinant of root-associated bacterial communities, but also observe a clear correlation with plant phylogeny and define a core root microbiome at this site.

The use of anammox microbiomes to treat wastewater is an escalating biotechnology, yet the functional role heterotrophic bacteria play in these systems remains poorly understood. Here, Lawsonet al. use metagenomics and metatranscriptomics to reveal that heterotrophs degrade free peptides, while recycling nitrate to nitrite.

The role of microbial diversity in ecosystems is less well understood than, for example, that of plant diversity. Analysing two independent data sets at a global and regional scale, Delgado-Baquerizo et al. show positive effects of soil diversity on multiple terrestrial ecosystem functions.

Coral-associated microbes could enhance the capacity of their host organism to respond to environmental change. Ziegler and colleagues use a reciprocal transplant experiment to show that microbiomes of heat-tolerant corals are more resilient to change than those of heat-sensitive corals.