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bioRxiv2020

Social survival: humpback whales (Megaptera novaeangliae) use social structure to partition ecological niches within proposed critical habitat

Animal culture and social bonds are relevant to wildlife conservation because they influence patterns of geography, behavior, and strategies of survival. Numerous examples of socially-driven habitat partitioning and ecological-niche specialization can be found among vertebrates, including toothed whales. But such social-ecological dynamics, described here as social niche partitioning, are not known among baleen whales, whose societies -- particularly on foraging grounds -- are largely perceived as unstructured and incidental to matters of habitat use and conservation. However, through 16 years of behavioral and photo-identification observations of humpback whales (Megaptera novaeangliae) feeding within a fjord system in British Columbia, Canada, we have documented long-term pair bonds (lasting up to 12 years) as well as a complex societal structure, which corresponds closely to persistent patterns in feeding strategy, long-term site fidelity (extended seasonal occupancy and annual rate of return up to 75%), specific geographic preferences within the fjord system, and other forms of habitat use. Randomization tests of network congruency and clustering algorithms were used to test for overlap in patterns of social structure and habitat use, which confirmed the occurrence of social niche partitioning on the feeding grounds of this baleen whale. In addition, we document the extensive practice of group bubble net feeding in Pacific Canada. This coordinated feeding behavior was found to strongly mediate the social structure and habitat use within this humpback whale society. Additionally, during our 2004 - 2019 study, we observed a shift in social network structure in 2010 - 2012, which corresponded with environmental and demographic shifts including a sudden decline in the populations calving rate. Our findings indicate that the social lives of humpback whales, and perhaps baleen whales generally, are more complex than previously supposed and should be a primary consideration in the assessment of potential impacts to important habitat.

animal behavior and cognition↗

bioRxiv2021

Taxonomic, ecological and morphological diversity of Ponto-Caspian gammaridean amphipods: a review

Thanks to its dynamic geological history the Ponto-Caspian region harbors a unique and unusually adaptable fauna, notorious for its invasive species. Gammarid amphipods attained considerable diversity, becoming the worlds second most speciose ancient-lake amphipod radiation. Nonetheless, apart from a few invasive species, this group remains poorly studied. Herein, we review and quantify the taxonomic, morphological and ecological diversity, as well as phylogenetic context of Ponto-Caspian gammarids within the adaptive radiation framework. Published molecular phylogenies indicate that this radiation has a monophyletic mid-Miocene Paratethyan origin, and is nested within the morphologically-conserved Atlanto-Mediterranean genus Echinogammarus. We find extensive disparity in body shape, size, ornamentation and appendage length, along a broad ecological gradient from mountain springs to depths exceeding 500 m, on virtually all substrate types (including symbiosis). We propose four putative ecomorphs that appear convergent with distantly related oceanic and Baikal Lake taxa. Thus, the identified patterns support the adaptive radiation model, although extensive further research is needed. A checklist and provisional key to all known endemic species are provided to facilitate taxonomic research. Ponto-Caspian gammarids could be a potentially powerful model for studying adaptive radiations and invasive species evolution.

zoology↗

bioRxiv2021

Metagenomic screening for lipolytic genes reveals an ecology-clustered distribution pattern

Lipolytic enzymes are one of the most important enzyme types for application in various industrial processes. Despite the continuously increasing demand, only a small portion of the so far encountered lipolytic enzymes exhibit adequate stability and activities for biotechnological applications. To explore novel and/or extremophilic lipolytic enzymes, microbial consortia in two composts at thermophilic stage were analyzed using function-driven and sequence-based metagenomic approaches. Analysis of community composition by amplicon-based 16S rRNA genes and transcripts, and direct metagenome sequencing revealed that the communities of the compost samples were dominated by members of the phyla Actinobacteria, Proteobacteria, Firmicutes, Bacteroidetes and Chloroflexi. Function-driven screening of the metagenomic libraries constructed from the two samples yielded 115 unique genes encoding lipolytic enzymes. The family assignment of these enzymes was conducted by analyzing the phylogenetic relationship and generation of a protein sequence similarity network according to an integral classification system. The sequence-based screening was performed by using a newly developed database, containing a set of profile Hidden Markov models, highly sensitive and specific for detection of lipolytic enzymes. By comparing the lipolytic enzymes identified through both approaches, we demonstrated that the activity-directed complements sequence-based detection, and vice versa. The sequence-based comparative analysis of lipolytic genes regarding diversity, function and taxonomic origin derived from 175 metagenomes indicated significant differences between habitats. Analysis of the prevalent and distinct microbial groups providing the lipolytic genes revealed characteristic patterns and groups driven by ecological factors. The here presented data suggests that the diversity and distribution of lipolytic genes in metagenomes of various habitats are largely constrained by ecological factors.

microbiology↗

bioRxiv2021

Adaptive maternal effects in early life history traits help to maintain ecological resilience in novel environments for two contrasting Senecio species

While many organisms shift their development plastically to maintain fitness as environments change, such plasticity has limits. Population mean fitness is expected to decline when novel environments exceed the limits to plasticity, but the level of fitness costs is expected to vary among genotypes that can increase adaptive potential. We lack fundamental insights into how and when changes in early development traits increase adaptive potential in novel environments, which limits our ability to predict the response of natural populations to global change. To test whether genetic variation in development time is associated with increased adaptive potential in novel environments, we used a breeding design to generate c.20,000 seeds of two ecologically contrasting Sicilian species of daisies (Senecio, Asteraceae) adapted to high and low elevations on Mount Etna. We planted the seeds across four elevations that included the native range of each species, and a novel elevation. We tracked seedling mortality and measured development time as the number of days it took seedlings to establish. As predicted, genetic variance in survival increased at novel elevations. However, genetic variance in development time showed the opposite trend, decreasing at novel elevations. A strong negative genetic correlation between development time in the native range and survival at novel elevations suggested that genotypes with faster development in native environments survived better in novel environments. These results were consistent across the two ecologically contrasting species, suggesting that genetic variance in early development in native environments could be used to predict population responses to novel environments.

evolutionary biology↗

bioRxiv2021

An ecological basis for dual genetic code expansion in marine deltaproteobacteria

Marine benthic environments may be shaped by anthropogenic and other localized events, leading to changes in microbial community composition evident decades after a disturbance. Marine sediments in particular harbor exceptional taxonomic diversity and can shed light on distinctive evolutionary strategies. Genetic code expansion may increase the structural and functional diversity of proteins in cells, by repurposing stop codons to encode noncanonical amino acids: pyrrolysine (Pyl) and selenocysteine (Sec). Here, we show that the genomes of abundant Deltaproteobacteria from the sediments of a deep-ocean chemical waste dump site, have undergone genetic code expansion. Pyl and Sec in these organisms appear to augment trimethylamine (TMA) and one-carbon metabolism, representing key drivers of their ecology. The inferred metabolism of these sulfate-reducing bacteria places them in competition with methylotrophic methanogens for TMA, a contention further supported by earlier isotope tracer studies and reanalysis of metatranscriptomic studies. A survey of genomic data further reveals a broad geographic distribution of a niche group of similarly specialized Deltaproteobacteria including at sulfidic sites in the Atlantic Ocean, Gulf of Mexico, Guayamas Basin, and North Sea, as well as in terrestrial and estuarine environments. These findings reveal an important biogeochemical role for specialized Deltaproteobacteria at the interface of the carbon, nitrogen and sulfur cycles, with their niche adaptation and ecological success seemingly enabled by genetic code expansion.

microbiology↗

bioRxiv2021

Assessing the origins of the European Plagues following the Black Death: a synthesis of genomic, historical and ecological information

The Second Plague Pandemic started in Europe with the Black Death in 1346 and lasted until the 19th century. Based on ancient DNA studies, there is a scientific disagreement over whether the bacterium, Yersinia pestis, came into Europe once (Hypothesis 1), or repeatedly over the following four centuries (Hypothesis 2). Here we synthesize the most updated phylogeny together with historical, archeological, evolutionary and ecological information. On the basis of this holistic view, we conclude that Hypothesis 2 is the most plausible. We also suggest that Y. pestis lineages might have developed attenuated virulence during transmission, which can explain the convergent evolutionary signals, including pla-decay, that appeared at the end of the pandemics. Significance StatementOver the last few years there has been a great deal of scientific debate regarding whether the plague bacterium, Yersinia pestis, spread from a Western European reservoir during the Second Plague Pandemic, or if it repeatedly came to Europe from Asia. Here we make a synthesis of the available evidence, including genomes of ancient DNA, historical, archeological and ecological information. We conclude that the bacterium most likely came to Europe from Asia several times during the Second Plague Pandemic.

evolutionary biology↗

bioRxiv2021

Ecological basis and genetic architecture of crypsis polymorphism in the desert clicker grasshopper (Ligurotettix coquilletti)

Color polymorphic species can offer exceptional insight into the ecology and genetics of adaptation. Although the genetic architecture of animal coloration is diverse, many color polymorphisms are associated with large structural variants and maintained by biotic interactions. Grasshoppers are exceptionally polymorphic in both color and karyotype, making them excellent models for understanding the ecological drivers and genetic underpinnings of color variation. Banded and uniform morphs of the desert clicker grasshopper (Ligurotettix coquilletti) are found across the western deserts of North America. To address the hypothesis that predation maintains local color polymorphism and shapes regional crypsis variation, we surveyed morph frequencies and tested for covariation with two predation environments. Morphs coexisted at intermediate frequencies at most sites, consistent with local balancing selection. Morph frequencies covaried with the appearance of desert substrate - an environment used only by females - indicating that ground-foraging predators are major agents of selection on crypsis. We next addressed the hypothesized link between morph variation and genome structure. To do so, we designed an approach for detecting inversions and indels using only RADseq data. The banded morph was perfectly correlated with a large putative indel. Remarkably, indel dominance differed among populations, a rare example of dominance evolution in nature.

evolutionary biology↗

bioRxiv2021

A role for ecologically-tuned chunking in the evolution of advanced cognition demonstrated by modelling the cleaner fish market problem

What makes cognition advanced is an open and not precisely defined question. One perspective involves increasing the complexity of associative learning, from conditioning to learning sequences of events ( chaining) to representing various cue combinations as chunks. Here we develop a weighted-graph model to study the conditions for the evolution of chunking ability, based on the ecology of the cleaner fish Labroides dimidiatus. Cleaners must learn to serve visitor clients before resident clients, because a visitor leaves if not attended while a resident waits for service. This challenge has been captured in various versions of the ephemeral-reward task, which has been proven difficult for a range of cognitively capable species. We show that chaining is the minimal requirement for solving the laboratory task, that involves repeated simultaneous exposure to an ephemeral and permanent food source. Adding ephemeral-ephemeral and permanent-permanent combinations, as cleaners face in the wild, requires individuals to have chunking abilities to solve the task. Importantly, chunking parameters need to be calibrated to ecological conditions in order to produce adaptive decisions. Thus, it is the fine tuning of this ability which may be the major target of selection during the evolution of advanced associative learning.

animal behavior and cognition↗

bioRxiv2021

Secondary metabolism drives ecological breadth in the Xylariaceae

Global, large-scale surveys of phylogenetically diverse plant and lichen hosts have revealed an extremely high richness of endophytes in the Xylariales, one of the largest clades of filamentous fungi and a significant source of novel secondary metabolites (SMs). Endophytes may produce host protective antimicrobial or insecticidal SMs, as well as compounds that facilitate symbiotic establishment through suppression or degradation of host immune response, but the ecological roles of most SMs are unknown. Here we characterized metabolic gene clusters in 96 genomes of endophytes and closely related saprotrophs and pathogens in two clades of Xylariales (Xylariaceae s.l. and Hypoxylaceae). Hundreds of genes appear horizontally transferred to xylarialean fungi from distantly related fungi and bacteria, including numerous genes in secondary metabolite gene clusters (SMGCs). Although all xylarialean genomes contain hyperabundant SMGCs, we show that increased gene duplications, horizontal gene transfers (HGTs), and SMGC content in Xylariaceae s.l. taxa are linked to greater phylogenetic host breadth, larger biogeographic distributions, and increased capacity for lignocellulose decomposition compared to Hypoxylaceae taxa. Overall, our results suggest that xylarialean endophytes capable of dual ecological modes (symbiotic and saprotrophic) experience greater selection to diversify SMGCs to both increase competitiveness within microbial communities and facilitate diverse symbiotic interactions.

genomics↗

bioRxiv2021

In an "ecological-belonging" intervention to reduce inequities in STEM, context matters

Doubts about belonging in the classroom are often shouldered disproportionately by students from historically marginalized groups, which can lead to underperformance. Ecological-belonging interventions use a classroom-based activity to instill norms that adversity is normal, temporary and surmountable. Building on prior studies, we sought to identify the conditions under which such interventions are effective. In a chemistry course (Study 1), students from underrepresented ethnic backgrounds underperformed relative to their peers in the absence of the intervention. This performance gap was eliminated by the intervention. In an introductory biology course (Study 2), there were no large performance gaps in the absence of the intervention, and the intervention had no effect. Study 2 also explored the role of the instructor that delivers the intervention. The intervention boosted scores in classrooms of instructors with a fixed (versus growth-oriented) intelligence mindset. Our results suggest that ecological-belonging interventions are more effective in more threatening classroom contexts.

scientific communication and education↗

bioRxiv2021

Toward an understanding of the chemical ecology of alternative reproductive tactics in the bulb mite (Rhizoglyphus robini)

BackgroundUnder strong sexual selection, certain species evolve distinct intrasexual, alternative reproductive tactics (ARTs). In many cases, ARTs can be viewed as environmentally-cued threshold traits, such that ARTs coexist if their relative fitness alternates over the environmental cue gradient. Surprisingly, the chemical ecology of ARTs has been underexplored in this context. To our knowledge, no prior study has directly quantified pheromone production for ARTs in a male-polymorphic species. Here, we used the bulb mite--in which males are either armed fighters that kill conspecifics, or unarmed scramblers--as a model system to gain insight into the role of pheromones in the evolutionary maintenance of ARTs. Given that scramblers forgo investment into weaponry, we tested whether scramblers produce higher pheromone quantities than fighters, which would improve the fitness of the scrambler phenotype, e.g. through female mimicry to avoid aggression from competitors. To this end, we sampled mites from a rich and a poor nutritional environment and quantified their production of the female sex pheromone -acaridial through gas chromatography analysis. ResultsWe found a positive relationship between pheromone production and body size, but males exhibited a steeper slope in pheromone production with increasing size than females. Females exhibited a higher average pheromone production than males. We found no significant difference in slope of pheromone production over body size between fighters and scramblers. However, scramblers reached larger body sizes and higher pheromone production than fighters, providing some evidence for a potential female mimic strategy adopted by large scramblers. Pheromone production was significantly higher in mites from the rich nutritional environment than the poor environment. ConclusionFurther elucidation of pheromone functionality in bulb mites, and additional inter-and intrasexual comparisons of pheromone profiles are needed to determine if the observed intersexual and intrasexual differences in pheromone production are adaptive, if they are a by-product of allometric scaling, or diet-mediated pheromone production under weak selection. We argue chemical ecology offers a novel perspective for research on ARTs and other complex life-history traits.

evolutionary biology↗

bioRxiv2021

Ecological inference using data from accelerometers needs careful protocols

O_LIAccelerometers in animal-attached tags have proven to be powerful tools in behavioural ecology, being used to determine behaviour and provide proxies for movement-based energy expenditure. Researchers are collecting and archiving data across systems, seasons and device types. However, in order to use data repositories to draw ecological inference, we need to establish the error introduced according to sensor type and position on the study animal and establish protocols for error assessment and minimization. C_LIO_LIUsing laboratory trials, we examine the absolute accuracy of tri-axial accelerometers and determine how inaccuracies impact measurements of dynamic body acceleration (DBA), as the main acceleration-based proxy for energy expenditure. We then examine how tag type and placement affect the acceleration signal in birds using (i) pigeons Columba livia flying in a wind tunnel, with tags mounted simultaneously in two positions, (ii) back- and tail-mounted tags deployed on wild kittiwakes Rissa tridactyla. Finally, we (iii) present a case study where two generations of tag were deployed using different attachment procedures on red-tailed tropicbirds Phaethon rubricauda foraging in different seasons. C_LIO_LIBench tests showed that individual acceleration axes required a two-level correction (representing up to 4.3% of the total value) to eliminate measurement error. This resulted in DBA differences of up to 5% between calibrated and uncalibrated tags for humans walking at different speeds. Device position was associated with greater variation in DBA, with upper- and lower back-mounted tags in pigeons varying by 9%, and tail- and back-mounted tags varying by 13% in kittiwakes. Finally, DBA varied by 25% in tropicbirds between seasons, which may be attributable to tag attachment procedures. C_LIO_LIAccelerometer accuracy, tag placement, and attachment details critically affect the signal amplitude and thereby the ability of the system to detect biologically meaningful phenomena. We propose a simple method to calibrate accelerometers that should be used prior to deployments and archived with resulting data, suggest a way that researchers can assess accuracy in previously collected data, and caution that variable tag placement and attachment can increase sensor noise and even generate trends that have no biological meaning. C_LI

animal behavior and cognition↗

bioRxiv2021

Effect of the Ecological Location of a Water Source on Entropy and other Spatio-temporal Behavioral Features: An extended and systematic replication

In behavior analysis, the modulation of the effect of time-based schedules by the spatial characteristics of the environment has been scarcely studied. Furthermore, the spatial organization of behavior, despite its ubiquity and ecological relevance, has not been widely addressed. The purpose of the present work was to analyze the effect of water delivery location (peripheral vs. central) on the spatial organization of water-feeding behavior under time-based schedules. One group of rats was exposed to a Fixed Time 30 s-water-delivery schedule and a second group to a Variable Time 30 s schedule. For both groups, in the first phase, the water dispenser was located in the perimetral zone. In the second condition, the water dispenser was located in the central zone. Each location was presented for 20 sessions. Rats trajectories, distance to the dispenser, accumulated time in regions, and entropy measures were analyzed. A differential effect of the location of water delivery in interaction with the time-based schedule was observed on all the analyzed spatial qualities of behavior. The findings are discussed in relation to the ecological proposal of Timberlakes behavioral systems.

animal behavior and cognition↗

bioRxiv2021

Ecological specialization, rather than the island rule, explains morphological diversification in an ancient radiation of geckos

Island colonists are often assumed to experience higher levels of phenotypic diversification than continental taxa. However, empirical evidence has uncovered exceptions to this "island effect". Here, we tested this pattern using the geckos of the genus Pristurus from continental Arabia and Africa and the Socotra Archipelago. Using a recently published phylogeny and an extensive morphological dataset, we explore the differences in phenotypic evolution between Socotran and continental taxa. Moreover, we reconstructed ancestral habitat occupancy to examine if ecological specialisation is correlated with morphological change, comparing phenotypic disparity and trait evolution between habitats. We found a heterogeneous outcome of island colonisation. Namely, only one of the three colonisation events resulted in a body size increase. However, in general, Socotran species do not present higher levels or rates of morphological diversification than continental groups. Instead, habitat specialisation explains better the body size and shape evolution in Pristurus. Particularly, the colonisation of ground habitats appears as the main driver of morphological change, producing the highest disparity and evolutionary rates. Additionally, arboreal species show very similar body size and head proportions. These results reveal a determinant role of ecological mechanisms in morphological evolution and corroborate the complexity of ecomorphological dynamics in continent-island systems.

evolutionary biology↗

bioRxiv2021

One Health or Three? Transmission modelling of Klebsiella isolates reveals ecological barriers to transmission between humans, animals and the environment

The Klebsiella group is highly diverse both genetically and ecologically, being commonly recovered from humans, livestock, plants, soil, water, and wild animals. Many species are opportunistic pathogens, and can harbour diverse classes of antimicrobial resistance (AMR) genes. K. pneumoniae is responsible for a high public-health burden, due in part to the rapid spread of health-care associated clones that are non-susceptible to carbapenems. Klebsiella thus represents a highly pertinent taxon for assessing the risk to public health posed by animal and environmental reservoirs. Here we report an analysis of 6548 samples and 3,482 genome sequences representing 15 Klebsiella species sampled over a 15-month period from a wide range of clinical, community, animal and environmental settings in and around the city of Pavia, in the northern Italian region of Lombardy. Despite carbapenem-resistant clones circulating at a high frequency in the hospitals, we find no genotypic or phenotypic evidence for non-susceptibility to carbapenems outside of the clinical environment. The non-random distribution of species and strains across sources point to ecological barriers that are likely to limit AMR transmission. Although we find evidence for occasional transmission between settings, hierarchical modelling and intervention analysis suggests that direct transmission from the multiple non-human (animal and environmental) sources included in our sample accounts for less than 1% of hospital disease, with the vast majority of clinical cases originating from other humans.

microbiology↗

bioRxiv2021

What ecological factors favor parthenogenesis over sexual reproduction? A study on the facultatively parthenogenetic mayfly Alainites muticus in natural populations.

Different reproductive modes are characterized by costs and benefits which often depend on ecological contexts. Benefits of sex are expected to increase under complex biotic interactions, whereas parthenogenesis can be beneficial for reproductive assurance when females are mate limited. Here, we study how different ecological contexts influence the frequency of sex or parthenogenesis in the facultatively parthenogenetic mayfly Alainites muticus. We first verified that high parthenogenetic frequencies translate into female-biased population sex ratios. We then measured the population sex ratio (a proxy for parthenogenetic capacities), density of individuals (mate limitation) and community diversity (biotic interaction complexity) for 159 A. muticus populations, and used structural equation modeling to investigate their direct and indirect influences on sex ratios. We found no effect of community diversity or altitude on sex ratios. Furthermore, even when females can reproduce parthenogenetically, they generally reproduce sexually, indicating that the benefits of sex exceed its costs in most situations. Sex ratios become female-biased in low population densities, as expected if mate limitation selects for parthenogenesis. Mate limitation might be widespread in mayflies because of their very short adult lifespan and limited dispersal, which can generate strong selection for reproductive assurance and may provide a steppingstone towards obligate parthenogenesis.

evolutionary biology↗

bioRxiv2021

Little hope for the polyploid endemic Pyrenean Larkspur (Delphinium montanum): evidences from population genomics and Ecological Niche Modelling

Species endemic to restricted geographical ranges represent a particular conservation issue, be it for their heritage interest. In a context of global change, this is particularly the case for plants which belong to high-mountain ecosystems and, because of their ecological requirements, are doomed to survive or disappear on their sky islands. The Pyrenean Larkspur (Delphinium montanum, Ranunculaceae) is endemic to the Eastern part of the Pyrenees (France and Spain). It is now only observable at a dozen of localities and some populations show signs of decline, such as a recurrent lack of flowering. Implementing population genomic approach (e.g. RAD-seq like) is particularly useful to understand genomic patterns of diversity and differentiation in order to provide recommendations in term of conservation. However, it remains challenging for species such as D. montanum that are autotetraploid with a large genome size (1C-value > 10 pg) as most methods currently available were developed for diploid species. A Bayesian framework able to call genotypes with uncertainty allowed us to assess genetic diversity and population structure in this system. Our results show evidence for inbreeding (mean GIS = 0.361) within all the populations and substantial population structure (mean GST = 0.403) at the metapopulation level. In addition to a lack of connectivity between populations, spatial projections of Ecological Niche Modelling analyses under different climatic scenarios predict a dramatic decrease of suitable habitat for D. montanum in the future. Based on these results, we discuss the relevance and feasibility of different conservation measures.

evolutionary biology↗

bioRxiv2021

Ecological stochasticity and phage induction diversify bacterioplankton communities at the microscale

In many natural environments, microorganisms self-assemble around heterogeneously distributed resource patches. The growth and collapse of populations on resource patches can unfold within spatial ranges of a few hundred micrometers or less, making such microscale ecosystems hotspots of biological interactions and nutrient fluxes. Despite the potential importance of patch-level dynamics for the large-scale evolution and function of microbial communities, we have not yet been able to delineate the ecological processes that control natural populations at the microscale. Here, we addressed this challenge in the context of microbially-mediated degradation of particulate organic matter by characterizing the natural marine communities that assembled on over one thousand individual microscale chitin particles. Through shotgun metagenomics, we found significant variation in microscale community composition despite the similarity in initial species pools across replicates. Strikingly, a subset of particles was highly populated by rare chitin-degrading strains; we hypothesized that their conditional success reflected the impact of stochastic colonization and growth on community assembly. In contrast to the conserved functional structures that emerge in ecosystems at larger scales, this taxonomic variability translated to a wide range of predicted chitinolytic abilities and growth returns at the level of individual particles. We found that predation by temperate bacteriophages, especially of degrader strains, was a significant contributor to the variability in the bacterial compositions and yields observed across communities. Our study suggests that initial stochasticity in assembly states at the microscale, amplified through biotic interactions, may have significant consequences for the diversity and functionality of microbial communities at larger scales. Significance StatementThe biogeochemical consequences of the degradation of particulate organic matter by microorganisms represent the cumulative effect of microbial activity on individual microscale resource patches. The ecological processes controlling community dynamics in these highly localized microenvironments remain poorly understood. Here, we find that complex marine communities growing on microscale resource particles diverge both taxonomically and functionally despite assembling under identical abiotic conditions from a common species pool. We show that this variability stems from bacteriophage predation and history-dependent factors in community assembly, which create stochastic dynamics that are spatially structured at the microscale. This microscale stochasticity may have significant consequences for the coexistence, evolution, and function of diverse bacterial and viral populations in the global ocean.

microbiology↗