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bioRxiv2019

Habitat specificity is not universal proxy for sensitivity to habitat conversion among rodents on the Canadian Prairies

Converting habitat for agricultural production threatens biodiversity loss worldwide and has significant implications for human well-being. Debates on how to conserve biodiversity as the demand for agriculture products rises is being informed by studies using habitat specificity as a proxy for sensitivity to land modification, assuming all species respond to habitat loss and fragmentation relative to their affinity towards the habitat type being converted. Here, we test this assumption among rodent assemblages on the Canadian Prairies, hypothesizing negative responses among grassland obligates and neutral or positive responses among habitat generalists to landscape change along a gradient of increasing agricultural intensity. We found complex, sometimes contradictory responses among rodent species, which depended on the magnitude of habitat loss that had occurred and did not always reflect each species relative affinity for grassland habitat. Our results suggest future studies should avoid assuming a single habitat type appropriately characterizes resource limitation among all species, and instead carefully consider which dimension of the ecological niche defines specificity for each species. Our results indicate habitat specificity is not always a reliable proxy for sensitivity to land modification, with significant implications for biodiversity conservation when used to inform agriculture and land use policies.

ecology↗

bioRxiv2019

Emergence of alternative stable states in microbial communities in a fluctuating environment

The effect of environmental fluctuations is a major question in ecology. While it is widely accepted that fluctuations and other types of disturbances can increase biodiversity, we have only a limited understanding of the circumstances in which other types of outcomes can occur in a fluctuating environment. Here we explore this question with laboratory microcosms, using cocultures of two bacterial species, P. putida and P. veronii. At low dilution rates we observe competitive exclusion of P. veronii, whereas at high dilution rates we observe competitive exclusion of P. putida. When the dilution rate alternates between high and low, we do not observe coexistence between the species, but rather alternative stable states, in which only one species survives and initial species fractions determine the identity of the surviving species. The Lotka-Volterra model with a fluctuating mortality rate predicts that this outcome is independent of the timing of the fluctuations, and that the time-averaged mortality would also lead to alternative stable states, a prediction that we confirm experimentally. Other pairs of species can coexist in a fluctuating environment, and again consistent with the model we observe coexistence in the time-averaged dilution rate. We find a similar time-averaging result holds in a three-species community, highlighting that simple linear models can in some cases provide powerful insight into how communities will respond to environmental fluctuations.

ecology↗

bioRxiv2019

A Universal Phase Transition in Plankton Trait Dynamics

Key ecological traits, like cell size, often follow scale-free or self-similar distributions. This indicates that these systems might operate near a critical (i.e. second-order) phase transition where macroscopic system behaviour is largely decoupled from microscopic system details, allowing an extremely simple, yet accurate and robust mathematical system characterisation. However, how trait-distribution scaling results from a critical transition has not yet been explicitly demonstrated. Here, we demonstrate that a generic class of cell growth and division models exhibits a critical transition from a growth-dominated to a division-dominated phase. We find experimental evidence for this transition, both in the population dynamics and in the moment scaling of chlorophyll distributions, for prokaryotic and eukaryotic phytoplankton growth under different light intensities. Our approach offers testable predictions of the response of unicellular trait-distributions to perturbations.

ecology↗

bioRxiv2019

Depth and location influence prokaryotic and eukaryotic microbial community structure in New Zealand fjords

Systems with strong horizontal and vertical gradients, such as fjords, are useful models for studying environmental forcing. Here we examine microbial (prokaryotic and eukaryotic) community changes associated with the surface low salinity layer (LSL) and underlying seawater in multiple fjords in Fiordland National Park (New Zealand). High rainfall (1200-8000 mm annually) and linked runoff from native forested catchments results in surface LSLs with high tannin concentrations within each fjord. These gradients are expected to drive changes in microbial communities. We used amplicon sequencing (16S and 18S) to assess the impact of these gradients on microbial communities and identified depth linked changes in diversity and community structure. With increasing depth we observed significant increases in Proteobacteria (15%) and SAR (37%), decreases in Opisthokonta (35%), and transiently increased Bacteroidetes (3% increase from 0 to 40 m, decreasing by 8% at 200 m). Community structure differences were observed along a transect from inner to outer regions, specifically 25% mean relative abundance decreases in Opisthokonta and Bacteroidetes, and increases in SAR (25%) and Proteobacteria (>5%) at the surface, indicating changes based on distance from the ocean. This provides the first in-depth view into the ecological drivers of microbial communities within New Zealand fjords.

ecology↗

bioRxiv2019

Optimal foraging of benthic diatoms evolving novel movement behaviours

Adaptive locomotion of living organisms contributes to their competitive abilities and helps maintain their fitness in diverse environments. To date, however, our understanding of searching behavior and its ultimate cause remains poorly understood in ecology and biology. Here, we investigate motion patterns of biofilm-inhabiting marine raphid diatom Navicula arenaria var. rostellata in two-dimensional space. We report that individual Navicula cells display a "circular run-and-reversal" movement behavior at different concentrations of dissolved silicic acid (dSi). We show that gliding motions of cells can be predicted accurately with a universal Langevin model. Our experimental results are consistent with an optimal foraging strategy and a maximized diffusivity of the theoretical outcomes in which both circular-run and reversal behaviors are important ingredients. Our theoretical results suggest that the evolving movement behaviors of diatoms may be driven by optimization of searching behavioral strategy, and predicted behavioral parameters coincide with the experimental observations. These optimized movement behaviors are an evolutionarily stable strategy to cope with environmental complexity. ONE SENTENCE SUMMARYNovel experiments and modelling reveal that raphid diatoms can actively exploit resources in complex environments by adjusting their movement behavior.

ecology↗

bioRxiv2019

Changes in social cohesion in a long-lived species under a perturbation regime

O_LIUnderstanding the behaviour of a population under perturbations is crucial and can help to mitigate the effects of global change. Sociality can influence the dynamics of behavioural processes and plays an important role on populations resilience. However little is known about the effects of perturbations on the social cohesion of group-living animals.\nC_LIO_LITo explore the strength of social cohesion and its dynamics under perturbations, we studied an ecological system involving a colonial, long-lived species living in a site experiencing a shift to a perturbed regime. This regime, caused by the invasion of predators, led this colony to hold from 70% to only 3% of the total world population in only one decade. Because birds breed aggregated in discrete and annually changing patches within large colonies, we could disentangle whether annual aggregation was random or resulted from social bonding among individuals. Our goals were 1) to uncover if there was any long-term social bonding between individuals and 2) to examine whether the perturbation regime affected social cohesion.\nC_LIO_LIWe explored social cohesion by means of contingency tables and, within the Social Network Analysis framework, by modeling interdependencies among observations using additive and multiplicative effects (AME) and accounted for missing data. We analysed 25 years of monitoring with an individual capture-recapture database of more than 3,500 individuals.\nC_LIO_LIWe showed that social bonding occurs over years in this species. We additionally show that social bonding strongly decreased after the perturbation regime. We propose that sociality and individual behavioural heterogeneity have been playing a major role driving dispersal and thus population dynamics over the study period.\nC_LIO_LIPerturbations may lead not only to changes in individuals behaviours and fitness but also to a change in populations social cohesion. The demographic consequences of the breaking down of social bonds are still not well understood, but they can be critical for population dynamics of social species. Further studies considering individual heterogeneity, sociality and different types of perturbations should be carried out to improve our understanding on the resilience of social species.\nC_LI

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bioRxiv2019

Rolling stones gather moss: Movement and longevity of moss balls on an Alaskan glacier

Glaciers support diverse ecosystems that are largely comprised of microbial life. However, at larger, macroscopic scales, glacier moss balls (sometimes called "glacier mice") can develop from impurities on ice surfaces and represent a relatively rare biological phenomenon. These ovoid-shaped conglomerations of dirt and moss are only found on some glacier surfaces and provide key habitats for invertebrate colonization. Yet, despite their development and presence being widely reported, no targeted studies of their movement and persistence across years have been conducted. This knowledge gap is particularly important when considering the degree to which glacier moss balls may represent viable, long-term biotic habitats on glaciers, perhaps complete with their own ecological succession dynamics. Here, we describe the movement and persistence of glacier moss balls on the Root Glacier in southcentral Alaska, USA. We show that glacier moss balls move an average of 2.5 cm per day in herd-like fashion, and their movements are positively correlated with glacier ablation. Surprisingly, the dominant moss ball movement direction does not align with the prevailing wind or downslope directions, nor with any dominant direction of solar radiation. After attaining a mature size, glacier moss balls persist for many years, likely in excess of 6 years. Finally, we observed moss ball formation on the Root Glacier to occur within a narrow, low albedo stripe downwind of a nunatuk, a potential key source of moss spores and/or fine-grained sediment that interact to promote their formation.

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bioRxiv2019

Higher Temperatures Generically Favor Slower-Growing Bacterial Species in Multispecies Communities

Temperature is among the cardinal environmental variables which determine the composition and function of microbial communities. Many culture-independent studies have characterized communities that are affected by changing temperatures, either due to seasonal cycles1-3, long-term warming4-6, or latitudinal/elevational gradients7-8. However, a predictive understanding of how microbial communities respond to such changes in temperature is still lacking, partly because it is not obvious which aspects of microbial physiology determine whether a species should benefit from temperature alteration. Here, we incorporate how microbial growth rates change with temperature to a modified Lotka-Volterra competition model9, and predict that higher temperatures should generically favor slower-growing species in a bacterial community. We experimentally confirm this prediction in pairwise cocultures assembled from a diverse set of species, and we show that these changes to pairwise outcomes with temperature are also predictive of changing outcomes in three-species communities, suggesting our theory may propagate to more complex assemblages. Our results demonstrate that it is possible to predict how bacterial communities will shift with temperature knowing only the growth rates of the community members. These results provide a testable hypothesis for future studies of more complex, natural communities, and we hope that this work will help bridge the gap between ecological theory and the complex dynamics observed in metagenomic surveys.

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bioRxiv2019

Maternal effects and environmental filtering shape seed fungal communities in oak trees

O_LITrees, as foundation species, play a pivotal role in the species interaction networks that constitute forest ecosystems. From the seed stage, they interact with microbial communities that affect their growth, health and fitness. Despite their eco-evolutionary importance, the processes shaping seed microbial communities in natural forests have received little attention.\nC_LIO_LITo unravel these processes, we analyzed the microbial communities of seeds collected in populations of sessile oak (Quercus petraea) growing along elevation gradients. We focused on the fungal communities as this group includes seed pathogens. Ecological processes shaping the communities were quantified using joint species distribution models.\nC_LIO_LIFungi were present in all seed tissues, including the embryo. Fungal communities differed significantly among oak populations along the elevation gradients, and among mother trees within the same population. These maternal effects remained significant after seed fall, despite colonization by fungal species on the ground. Associations between tree pathogens and their antagonists were detected in the seeds.\nC_LIO_LIOur results demonstrate that both maternal effects and environmental filtering shape seed microbial communities of sessile oak. They provide a starting point for future research aimed at identifying the seed extended phenotypic traits that influence seed dispersal and germination, and seedling survival and growth across environments.\nC_LI

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bioRxiv2019

Are Railways detrimental to bird populations? A BDACI study on the Construction of the Bothnia Line Railway

Railways, like roads, are commonly considered bad for birdlife, but supporting data are very scarce. We conducted a 14-year before-during-after control-impact (BDACI) study of birds in agricultural landscapes affected by the construction of the Bothnia Line Railway (BLR) in northern Sweden. The \"during\" phase was split into two phases, one for the true construction period and one for the years when the railway was ready but not trafficked. Avian biodiversity increased in impact sites (N=13), but not in control sites (N=6). The numbers of breeding territories decreased correspondingly in impact and control sites, but trends differed between species and sites. Developments in the Degernas site demonstrated that mitigation could be successful. Finally, there was no support for a shying-away effect of the BLR. Territory midpoints moved closer rather than away from the railway, albeit with variable patterns for individual sites and species. Mixed effect models showed no differences in avian biodiversity between the Construction, Ready and Traffic phases compared with Before, but relative increases in numbers of territories and decreases in territory midpoint distances to the BLR. The results do not support a general detrimental effect of railway construction on bird populations in terms of biodiversity loss, reduced abundances or shying-away from train traffic. More studies and the development of \"Railway Ecology\" are badly needed.

ecology↗

bioRxiv2019

Variations in terrestrial arthropod DNA metabarcoding methods recovers robust beta diversity but variable richness and site indicators based on exact sequence variants

Terrestrial arthropod fauna have been suggested as a key indicator of ecological integrity in forest systems. Because phenotypic identification is expert-limited, a shift towards DNA metabarcoding could improve scalability and democratize the use of forest floor arthropods for biomonitoring applications. The objective of this study was to establish the level of field sampling and DNA extraction replication needed for soil arthropod biodiversity assessments. Processing individually collected field samples recovered significantly higher richness (539-596 ESVs) than pooling the same number of field samples (126-154 ESVs), and we found no significant richness differences when using 1 or 3 pooled DNA extractions. Variations in the number of individual or composite samples or DNA extractions resulted in similar sample clustering based on community dissimilarities. Though our ability to identify taxa to species rank was limited, we were able to use arthropod COI metabarcodes from forest soil to assess richness, distinguish among sites, and recover site indicators based on unnamed exact sequence variants. Our results highlight the need to continue DNA barcoding of local taxa during COI metabarcoding studies to help build reference databases. All together, these sampling considerations support the use of soil arthropod COI metabarcoding as a scalable method for biomonitoring.

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bioRxiv2019

Lek-associated movement of a putative Ebolavirus reservoir, the Hammer-headed fruit bat (Hypsignathus monstrosus), in northern Republic of Congo

The biology and ecology of Africas largest fruit bat remains largely understudied and enigmatic despite at least two highly unusual attributes. The acoustic lek mating behavior of the hammer-headed bat (Hypsignathus monstrosus) in the Congo basin was first described in the 1970s. Then in the 2000s, molecular testing implicated this species and other fruit bats as potential reservoir hosts for Ebola virus and it was one of only two fruit bat species epidemiologically linked to the 2008 Luebo, Democratic Republic of Congo, Ebola outbreak. Here we share findings from the first pilot study of hammer-headed bat movement using GPS tracking and accelerometry units and a small preceding radio-tracking trial at an apparent lekking site. The radio-tracking revealed adult males had high rates of nightly visitation to the site compared to females (only one visit) and that two of six females day-roosted [~]100 m west of Libonga, the nearest village that is [~]1.6 km southwest. Four months later, in mid-April 2018, five individual bats, comprised of four males and one female, were tracked from two to 306 days, collecting from 67 to 1022 GPS locations. As measured by mean distance to the site and proportion of nightly GPS locations within 1 km of the site (percent visitation), the males were much more closely associated with the site (mean distance 1.4 km; 51% visitation), than the female (mean 5.5 km; 2.2% visitation). Despite the small sample size, our tracking evidence supports our original characterization of the site as a lek, and the lek itself is much more central to male than female movement. Moreover, our pilot demonstrates the technical feasibility of executing future studies on hammer-headed bats that will help fill problematic knowledge gaps about zoonotic spillover risks and the conservation needs of fruit bats across the continent.

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bioRxiv2019

Finding missing links in interaction networks

Documenting which species interact within ecological communities is challenging and labour-intensive. As a result, many interactions remain unrecorded, potentially distorting our understanding of network structure and dynamics. We test the utility of four structural models and a new coverage-deficit model for predicting missing links in both simulated and empirical bipartite networks. We find they can perform well, but that the predictive power of structural models varies with the underlying network structure. Predictions can be improved by ensembling multiple models. Sample-coverage estimators of the number of missed interactions are highly correlated with the number of missed interactions, but strongly biased towards underestimating the true number of missing links. Augmenting observed networks with most-likely missing links improves estimates of qualitative network metrics. Tools to identify likely missing links can be simple to implement, allowing the prioritisation of research effort and more robust assessment of network properties.

ecology↗

bioRxiv2019

Modelling variation in bushmeat harvesting among seven African ecosystems using the Madingley Model: yield, survival and ecosystem impacts

In principle, both the maximum sustainable yields of bushmeat, and the ecosystem impacts of extracting those yields, are likely to vary among ecosystems due to differences in the structure and function of ecosystems, but the data necessary to estimate this variation is lacking. Here, we compare seven different ecosystems on a North-South latitudinal gradient in Central Africa in terms of their trophic structure and capacity to support yields from bushmeat harvesting, using the Madingley General Ecosystem Model. The only factor that varies across simulations of these ecosystems is the climate which drives differences in vegetation structure and function, leading in turn to differences in the structure of the ecological community that emerge from the model. In a series of experiments (n=30), we simulate constant proportional harvesting of small and medium-sized warm-bloodied heterotrophs (1-23kg) over 30 years, recording expected bushmeat yields, and impacts on ecosystem structure, including trophic structure. Predictions for animal densities and trophic structures in the pristine (no harvesting) case varied among the ecosystems, with implications for bushmeat harvesting. For example, wooded savannah ecosystems stood out as having the greatest pristine densities in the target groups (11000-12000 animals per kilometre squared), greatest yields (100% higher than the tropical forest and 1000% higher than the desert ecosystem), and were the most resilient to harvesting. By contrast, small and medium-sized endothermic heterotrophs contributed only a small proportion of heterotrophs in the desert ecosystem, and thus the potential for bushmeat harvesting here was low. In all ecosystems, harvesting at the rate that maximised yield (55-65% population per year, except for the southern desert ecosystem) had strong impacts, causing drastic reductions in target functional groups, coupled with increases in smaller- and larger-bodied animals. Forest and desert ecosystems were particularly sensitive. Overall, the results suggest that, even for similar functional groups, bushmeat harvesting policies will need to vary substantially among ecosystems - and show that general ecosystem models could be a useful tool in helping to guide these policies.

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bioRxiv2019

Seed-dispersal networks lose complexity in tropical forest fragments

Seed dispersal interactions involve key ecological processes in tropical forests that help to maintain ecosystem functioning. Yet this functionality may be threatened by increasing habitat loss, defaunation and fragmentation. However, generalist species, and their interactions, can benefit from the habitat change caused by human disturbance while more specialized interactions mostly disappear. Therefore changes in the structure of the local, within fragment, networks can be expected. Here we investigated how the structure of seed-dispersal networks changes along a gradient of increasing habitat fragmentation. We analysed 16 bird seed-dispersal assemblages from forest fragments of a biodiversity-rich ecosystem. We found significant species-, interaction- and network-area relationships, yet the later was determined by the number of species remaining in each community. The number of frugivorous bird and plant species, their interactions, and the number of links per species decreases as area is lost in the fragmented landscape. In contrast, network nestedness has a negative relationship with fragment area, suggesting an increasing generalization of the network structure in the gradient of fragmentation. Network specialization was not significantly affected by area, indicating that some network properties may be invariant to disturbance. Still, the local extinction of partner species, paralleled by a loss of interactions and specialist-specialist bird-plant seed dispersal associations suggests the functional homogenization of the system as area is lost. Our study provides empirical evidence for network-area relationships driven by the presence/absence of remnant species and the interactions they perform.\n\nRESUMOInteracoes de dispersao de sementes formam um processo ecologico chave em florestas tropicais onde colaboram na manutencao do funcionamento do ecossistema. Porem, esta funcionalidade pode estar ameacada pelo aumento na perda e fragmentacao do habitat. Enquanto especies generalistas e suas interacoes podem se beneficiar da mudanca de habitat causada por disturbios antropicos, interacoes envolvendo especies mais especialistas sao, na maioria, eliminadas. Desta forma, mudancas nas redes locais, dentro de fragmentos florestais, sao esperadas. Neste trabalho nos investigamos como a estrutura de redes de dispersao de sementes mudam em um gradiente de fragmentacao do habitat. Nos analisamos 16 comunidades de dispersao de sementes espacialmente explicitas e distribuidas em fragmentos florestais de um ecossistema rico em biodiversidade. Nos encontramos relacoes significativas entre a area do fragmento e especies, interacoes e estrutura das redes, sendo que o ultimo foi determinado pelo numero de especies remanescentes em cada comunidade. O numero de especies de aves frugivoras e plantas e as interacoes entre eles, bem como o numero de links por especie diminuiram significativamente conforme a area dos fragmentos e perdida. Por outro lado, o aninhamento da rede mostrou uma relacao negativa com a area do fragmento, sugerindo um aumento da generalizacao da estrutura das redes com a fragmentacao do habitat. No entanto, o grau de especializacao das redes nao foi afetado pela area, indicando que algumas propriedades de rede podem ser resistentes a perturbacao. Sendo assim, a extincao local de especies parceiras, conjuntamente com a perda das interacoes e associacoes planta-dispersor mais especializadas, sugere uma homogeneizacao do sistema conforme a area do fragmento e perdida. Nosso estudo fornece evidencias empiricas para as relacoes rede-area, sendo estas direcionadas pela presenca e/ou ausencia das especies remanescentes bem como das interacoes que estas realizam.

ecology↗

bioRxiv2019

Diatoms structure the plankton community based on selective segregation in the world’s ocean

Diatoms are a major component of phytoplankton, believed to be responsible for around 20% of the annual primary production on Earth. As abundant and ubiquitous organisms, they are known to establish biotic interactions with many other members of the plankton. Through analysis of co-occurrence networks derived from the Tara Oceans expedition that take into account the importance of both biotic and abiotic factors in shaping the spatial distributions of species, we show that only 13% of diatom pairwise associations are driven by environmental conditions, whereas the vast majority are independent of abiotic factors. In contrast to most other plankton groups, at a global scale diatoms display a much higher proportion of negative correlations with other organisms, particularly towards potential predators and parasites, suggesting that their biogeography is constrained by top down pressure. Genus level analyses indicate that abundant diatoms are not necessarily the most connected, and that species-specific abundance distribution patterns lead to negative associations with other organisms. In order to move forward in the biological interpretation of co-occurrence networks, an open access extensive literature survey of diatom biotic interactions was compiled, of which 18.5% were recovered in the computed network. This result reveals the extent of what likely remains to be discovered in the field of planktonic biotic interactions, even for one of the best known organismal groups.\n\nImportanceDiatoms are key phytoplankton in the modern ocean involved in numerous biotic interactions, ranging from symbiosis to predation and viral infection, which have considerable effects on global biogeochemical cycles. However, despite recent large-scale studies of plankton, we are still lacking a comprehensive picture of the diversity of diatom biotic interactions in the marine microbial community. Through the ecological interpretation of both inferred microbial association networks and available knowledge on diatom interactions compiled in an open access database, we propose an eco-systems level understanding of diatom interactions in the ocean.

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bioRxiv2019

How Sampling-Based Overdispersion Undermines India’s Tiger Monitoring Orthodoxy

Conservation agencies entrusted with recovery of iconic mammals may exaggerate population trends without adequate scientific evidence. Recently, such populations were termed as political populations in the conservation literature. We surmise that political populations emerge when agencies are pressured to report abundances at large spatial scales for species that are difficult to survey. Indian tiger conservation agencies use an experimental approach called double-sampling using index-calibration models. A recent, mathematical, study demonstrated the unreliability of this approach in the context of Indias tigers. Yet, this approach continues to be applied and even promoted by global tiger conservation agencies in other tiger range countries. In this article, we aim to: (1) discuss the ecological oddities emerging from results of Indias national tiger surveys, (2) demystify the mathematics underlying the problems of this survey methodology and (3) confront these findings with results from Indias recent national tiger survey of 2014. Our analyses show that the predictions of tiger abundance using sign-based indices reported in the 2014 survey in fact vary greatly and can be severely misleading and confirming the presence of high sampling-based overdispersion and parameter covariance. We call for species conservation initiatives to implement monitoring methods that are designed to clearly answer, a priori, scientific or management objectives instead of potentially implementing them as reactions to extraneous, social or fund raising pressures.

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bioRxiv2019

Viruses of the eukaryotic plankton are predicted to increase carbon export efficiency in the global sunlit ocean

The biological carbon pump, in which carbon fixed by photosynthesis is exported to the deep ocean through sinking, is a major process in Earths carbon cycle. The proportion of primary production that is exported is termed the carbon export efficiency (CEE). Based on in-lab or regional scale observations, viruses were previously suggested to affect the CEE (i.e., viral "shunt" and "shuttle"). In this study, we tested associations between viral community composition and CEE measured at a global scale. A regression model based on relative abundance of viral marker genes explained 67% of the variation in CEE. Viruses with high importance in the model were predicted to infect ecologically important hosts. These results are consistent with the view that the viral shunt and shuttle functions at a large scale and further imply that viruses likely act in this process in a way dependent on their hosts and ecosystem dynamics.

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