SEARCH · Search bioRxiv

Results for “Ecology”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 217 records · Page 12Linked to original sources

bioRxiv2018

Stability, incumbency and ecological reorganizationafter the Permian-Triassic mass extinction

The Permian-Triassic mass extinction (PTME) altered macroevolutionary land-scapes by removing incumbent biota. Here, using terrestrial paleocommunities of the Karoo Basin spanning the PTME, we show that a pre-extinction incumbent configuration of biotic interactions made significant ecological re-organizations or macroevolutionary innovations unlikely. The post-PTME ecosystem initially was more likely to be reorganized, but incumbency was re-established by the Middle Triassic. We argue that the stability of the pre-PTME ecosystem, its subsequent loss, and replacement, resulted from the in-fluence of community-level structure and dynamics on species evolution and survival.\n\nOne sentence summaryBiotic incumbency at the end of the Paleozoic, based on community functional organization, was destroyed by the Permian-Triassic mass extinction, allowing the development of novel community types.

paleontology↗

bioRxiv2018

Investigating the viral ecology of global bee communities with high-throughput metagenomics

Bee viral ecology is a fascinating emerging area of research: viruses exert a range of effects on their hosts, exacerbate the impacts of other environmental stressors, and, importantly, are readily shared across multiple bee species in a community. However, our understanding of bee viral communities is limited, as it is primarily derived from studies of North American and European Apis mellifera populations. Here, we examined viruses in populations of A. mellifera and 11 other bee species from 9 countries, across 5 continents and Oceania. We developed a novel pipeline to rapidly, inexpensively, and robustly screen for bee viruses. This pipeline includes purification of encapsulated RNA/DNA viruses, sequence-independent amplification, high throughput sequencing, integrated assembly of contigs, and filtering to identify contigs specifically corresponding to viral sequences. We identified sequences corresponding to (+)ssRNA, (-)ssRNA, dsRNA, and ssDNA viruses. Overall, we found 127 contigs corresponding to novel viruses (i.e. previously not observed in bees), with 29 represented by >0.1 % of the reads in a given sample. These viruses and viral families were distributed across multiple regions and species. This study provides a robust pipeline for metagenomics analysis of viruses, and greatly expands our understanding of the diversity of viruses found in bee communities.

genomics↗

bioRxiv2018

Agricultural Pollution Risks Influence Microbial Ecology in Honghu Lake

BackgroundAgricultural activities, such as stock-farming, planting industry, and fish aquaculture, can influence the physicochemistry and biology of freshwater lakes. However, the extent to which these agricultural activities, especially those that result in eutrophication and antibiotic pollution, effect water and sediment-associated microbial ecology, remains unclear.\n\nMethodsWe performed a geospatial analysis of water and sediment associated microbial community structure, as well as physicochemical parameters and antibiotic pollution, across 18 sites in Honghu lake, which range from impacted to less-impacted by agricultural pollution. Furthermore, the co-occurrence network of water and sediment were built and compared accorded to the agricultural activities.\n\nResultsPhysicochemical properties including TN, TP, NO3--N, and NO2--N were correlated with microbial compositional differences in water samples. Likewise, in sediment samples, Sed-OM and Sed-TN correlated with microbial diversity. Oxytetracycline and tetracycline concentration described the majority of the variance in taxonomic and predicted functional diversity between impacted and less-impacted sites in water and sediment samples, respectively. Finally, the structure of microbial co-associations was influenced by the eutrophication and antibiotic pollution.\n\nConclusionThese analyses of the composition and structure of water and sediment microbial communities in anthropologically-impacted lakes are imperative for effective environmental pollution monitoring. Likewise, the exploration of the associations between environmental variables (e.g. physicochemical properties, and antibiotics) and community structure is important in the assessment of lake water quality and its ability to sustain agriculture. These results show agricultural practices can negatively influence not only the physicochemical properties, but also the biodiversity of microbial communities associated with the Honghu lake ecosystem. And these results provide compelling evidence that the microbial community can be used as a sentinel of eutrophication and antibiotics pollution risk associated with agricultural activity; and that proper monitoring of this environment is vital to maintain a sustainable environment in Honghu lake.

microbiology↗

bioRxiv2018

Ecological and evolutionary consequences of viral plasticity

Viruses can infect any organism. Because viruses use the host machinery to replicate, their performance depends on the host physiological state. For bacteriophages, this host-viral performance link has been characterized empirically and with intracellular theories. Such theories are too detailed to be included in models that study host-phage interactions in the long term, which hinders our understanding of systems that range from pathogens infecting gut bacteria to marine phage shaping present and future oceans. Here, we combined data and models to study the short- and long-term consequences that host physiology has on bacteriophage performance. We compiled data showing the dependence of lytic-phage traits on host growth rate (viral phenotypic \"plasticity\") to deduce simple expressions representing such plasticity. We included these expressions in a standard host-phage model, to understand how viral plasticity can break the expected evolutionary trade-off between infection time and viral offspring number. Furthermore, viral plasticity influences dramatically dynamic scenarios (e.g. sudden nutrient pulses or host starvation). We show that the effect of plasticity on offspring number, not generation time, drives the phage ecological and evolutionary dynamics. Standard models do not account for this plasticity, which handicaps their predictability in realistic environments. Our results highlight the importance of viral plasticity to unravel host-phage interactions, and the need of laboratory and field experiments to characterize viral plastic responses across systems.

microbiology↗

bioRxiv2018

Supragingival plaque microbiome ecology and functional potential in the context of health and disease

To address the question of how microbial diversity and function in the oral cavities of children relates to caries diagnosis, we surveyed the supragingival plaque biofilm microbiome in 44 juvenile twin pairs. Using shotgun sequencing, we constructed a genome encyclopedia describing the core supragingival plaque microbiome. Caries phenotypes contained statistically significant enrichments in specific genome abundances and distinct community composition profiles including strain-level changes. Metabolic pathways that are statistically associated with caries include several sugar-associated phosphotransferase systems, antimicrobial resistance, and metal transport. Numerous closely-related previously-uncharacterized microbes had substantial variation in central metabolism, including the loss of biosynthetic pathways resulting in auxotrophy, changing the ecological role. We also describe the first complete Gracilibacteria genomes from the human microbiome. Caries is a microbial community metabolic disorder that cannot be described by a single etiology and our results provide the information needed for next generation diagnostic tools and therapeutics for caries.

microbiology↗

bioRxiv2018

The ecology of the Chloroflexi in full-scale activated sludge wastewater treatment plants

Filamentous bacteria belonging to the phylum Chloroflexi have received considerable attention in wastewater treatment systems for their suggested role in operational problem of impaired sludge settleability known as bulking. Their consistently high abundance in full-scale systems, even in the absence of bulking, indicates that they make a substantial contribution to the nutrient transformations during wastewater treatment. In this study, extensive 16S rRNA amplicon surveys of full-scale Danish WWTPs were screened to identify the most numerically important Chloroflexi genera. Fluorescence in situ hybridization probes were designed for their in situ characterization. All abundant phylotypes of the phylum were identified as facultative anaerobic chemoorganotrophs involved in fermentation of sugars. These groups were all filamentous but differed in their morphology and spatial arrangement. Candidatus Villigracilis was predominantly located within the activated sludge flocs, where they possibly have structural importance, and their abundance was relatively stable. Conversely, the abundance of Candidatus Amarolinea was highly dynamic, relative to other genera, sometimes reaching abundances in excess of 30% of the biovolume, suggesting their likely role in bulking episodes. This study gives an important insight into the role of Chloroflexi in WWTPs, thus contributing to the broader goal of understanding the ecology of these biotechnologically important systems.

microbiology↗

bioRxiv2018

Adversarial childhood events are associated with Sudden Infant Death Syndrome (SIDS): an ecological study

Sudden Infant Death Syndrome (SIDS) is the most common cause of postneonatal infant death. The allostatic load hypothesis posits that SIDS is the result of perinatal cumulative painful, stressful, or traumatic exposures that tax neonatal regulatory systems. To test it, we explored the relationships between SIDS and two common stressors, male neonatal circumcision (MNC) and prematurity, using latitudinal data from 15 countries and over 40 US states during the years 1999-2016. We used linear regression analyses and likelihood ratio tests to calculate the association between SIDS and the stressors. SIDS prevalence was significantly and positively correlated with MNC and prematurity rates. MNC explained 14.2% of the variability of SIDSs male bias in the US, reminiscent of the Jewish myth of Lilith, the killer of infant males. Combined, the stressors increased the likelihood of SIDS. Ecological analyses are useful to generate hypotheses but cannot provide strong evidence of causality. Biological plausibility is provided by a growing body of experimental and clinical evidence linking adversary preterm and early-life events with SIDS. Together with historical evidence, our findings emphasize the necessity of cohort studies that consider these environmental stressors with the aim of improving the identification of at-risk infants and reducing infant mortality.

pathology↗

bioRxiv2018

Detecting spatiotemporal pattern of tuberculosis and the relationship between ecological environment and tuberculosis, a spatial panel data analysis in Guangxi, China

Guangxi is one of the provinces having the highest reported incidence of tuberculosis (TB) in China. However, spatial and temporal pattern and causation of the situation are still unclear. In order to detect the spatiotemporal pattern of TB and the association with ecological environment factors in Guangxi Zhuang autonomous region, China, We performed a spatiotemporal analysis with prediction using time series analysis, Morans I global and local spatial autocorrelation statistics, and space-time scan statistics, to detect temporal and spatial clusters. Spatial panel models were employed to identify the influence factors. The time series analysis shows that the number of reported cases peaked in spring and summer and decreased in autumn and winter with the annual reported incidence of 113.1/100,000 population. Morans I global statistics were greater than 0 (0.363 - 0.536) during the study period. The most significant hot spots were mainly located in the central part. The east part exhibited a low-low relation. By spacetime scanning, the clusters identified were similar to that of the local autocorrelation statistics, and were clustered toward the early of 2016. Duration of sunshine, per capita gross domestic product (PGDP), the recovery rate of TB and participation rate of new cooperative medical care insurance in rural areas had a significant negative association with TB. In conclusion, the reported incidence of TB in Guangxi remains high. The main cluster was located in the central part of Guangxi, a region where promoting the productivity, improving TB treatment pathway and strengthening environmental protective measures (increasing sunshine exposure) are urgently needed.

epidemiology↗

bioRxiv2018

Metabolic Diversity within the Globally Abundant Marine Group II Euryarchaea Drives Ecological Patterns

Despite their discovery over 25 years ago, the Marine Group II Euryarchaea (MGII) have remained a difficult group of organisms to study, lacking cultured isolates and genome references. The MGII have been identified in marine samples from around the world and evidence supports a photoheterotrophic lifestyle combining phototrophy via proteorhodopsins with the remineralization of high molecular weight organic matter. Divided between two clades, the MGII have distinct ecological patterns that are not understood based on the limited number of available genomes. Here, I present the comparative genomic analysis of 250 MGII genomes, providing the most detailed view of these mesophilic archaea to-date. This analysis identified 17 distinct subclades including nine subclades that previously lacked reference genomes. The metabolic potential and distribution of the MGII genera revealed distinct roles in the environment, identifying algal-saccharide-degrading coastal subclades, protein-degrading oligotrophic surface ocean subclades, and mesopelagic subclades lacking proteorhodopsins common in all other subclades. This study redefines the MGII and provides an avenue for understanding the role these organisms play in the cycling of organic matter throughout the water column.

microbiology↗

bioRxiv2018

Rapid inference of direct interactions in large-scale ecological networks from heterogeneous microbial sequencing data

The recent explosion of metagenomic sequencing data opens the door towards the modeling of microbial ecosystems in unprecedented detail. In particular, co-occurrence based prediction of ecological interactions could strongly benefit from this development. However, current methods fall short on several fronts: univariate tools do not distinguish between direct and indirect interactions, resulting in excessive false positives, while approaches with better resolution are so far computationally highly limited. Furthermore, confounding variables typical for cross-study data sets are rarely addressed. We present FlashWeave, a new approach based on a flexible Probabilistic Graphical Models framework to infer highly resolved direct microbial interactions from massive heterogeneous microbial abundance data sets with seamless integration of metadata. On a variety of benchmarks, FlashWeave outperforms state-of-the-art methods by several orders of magnitude in terms of speed while generally providing increased accuracy. We apply FlashWeave to a cross-study data set of 69 818 publicly available human gut samples, resulting in one of the largest and most diverse models of microbial interactions in the human gut to date.

systems biology↗

bioRxiv2018

Avian diet and foraging ecology constrain foreign egg recognition and rejection

Egg rejection is the most common defense against avian brood parasitism in which the host either removes the parasitic egg or deserts the parasitized clutch. The ability to recognize and reject a parasitic egg depends on bill morphology, sensory systems, and cognition, all of which are also shaped by other selective processes, such as foraging. This begs the question whether specific phenotypes associated with different foraging strategies and diets may constrain or facilitate egg recognition and rejection. Here, we propose a novel hypothesis that host species phenotypes related to foraging ecology and diet impose morphological and sensory constraints on the evolution of egg rejection. We conducted a comparative analysis of the adult diets and egg rejection rates of 165 current host and non-host species and found species that consume an animal and fruit dominated diet rather than seeds and grains, forage arboreally rather than aerially, and possess relatively larger body sizes have significantly higher egg rejection rates. As predicted, these results suggest that phenotypes related to specific diets and foraging strategies may differentially constrain or facilitate evolution of host egg rejection defenses against avian brood parasitism.

animal behavior and cognition↗

bioRxiv2018

Microbial communities of the Mediterranean rocky coast: ecology and biotechnological potential

Microbial communities from harsh environments hold great promise as sources of biotechnologically-relevant strains. In the present work, we have deeply characterized the microorganisms from three different rocky locations of the Mediterranean coast, an environment characterised by being subjected to harsh conditions such as high levels of irradiation and large temperature and salinity fluctuations. Through culture-dependent and culture-independent techniques, we have retrieved a complete view of the ecology and functional aspects of these communities and assessed the biotechnological potential of the cultivable microorganisms. A culture-independent approach through high-throughput 16S rRNA amplicon sequencing revealed that all three locations display very similar microbial communities, suggesting that there is a stable community associated to the sampled region, with Stanieria cyanosphaera, Rubrobacter sp. and the families Flammeovirgaceae, Phyllobacteriaceae, Rhodobacteraceae and Trueperaceae being the most abundant taxa. Furthermore, shotgun metagenomic sequencing results were in concordance with the high-thoughput 16S rRNA, and allowed a description of the eukaryotic and archaeal members of the community, which were abundant in Ascomycota and halotolerant archaea, respectively. The culture-dependent approach yielded a collection of 100 isolates (mainly pigmented), out of which 12 displayed high antioxidant activities, as proved with two in vitro (hydrogen peroxide and DPPH) and an in vivo (model organism C. elegans) assays.

microbiology↗

bioRxiv2018

Targeting microbial arsenic resistance genes: a new bioinformatic toolkit informs arsenic ecology and evolution in soil genomes and metagenomes

Environmental resistomes include transferable microbial genes. One important resistome component is resistance to arsenic, a ubiquitous and toxic metalloid that can have negative and chronic consequences for human and animal health. The distribution of arsenic resistance and metabolism genes in the environment is not well understood. However, microbial communities and their resistomes mediate key transformations of arsenic that are expected to impact both biogeochemistry and local toxicity. We examined the phylogenetic diversity, genomic location (chromosome or plasmid), and biogeography of arsenic resistance and metabolism genes in 922 soil genomes and 38 metagenomes. To do so, we developed a bioinformatic toolkit that includes BLAST databases, hidden Markov models and resources for gene-targeted assembly of nine arsenic resistance and metabolism genes: acr3, aioA, arsB, arsC (grx), arsC (trx), arsD, arsM, arrA, and arxA. Though arsenic related genes were common, they were not universally detected, contradicting the common conjecture that all organisms have them. From major clades of arsenic related genes, we inferred their potential for horizontal and vertical transfer. Different types and proportions of genes were detected across soils, suggesting microbial community composition will, in part, determine local arsenic toxicity and biogeochemistry. While arsenic related genes were globally distributed, particular sequence variants were highly endemic (e.g., acr3), suggesting dispersal limitation. The gene encoding arsenic methylase arsM was unexpectedly abundant in soil metagenomes (median 48%), suggesting that it plays a prominent role in global arsenic biogeochemistry. Our analysis advances understanding of arsenic resistance, metabolism, and biogeochemistry, and our approach provides a roadmap for the ecological investigation of environmental resistomes.

microbiology↗

bioRxiv2018

Biofilm forming capabilities and protein secretion systems distinguish ecologically diverse lineages of Xanthomonas from rice

Xanthomonas oryzae is a devastating pathogen of rice worldwide, however, X. sontii and X. maliensis are its non-pathogenic counterparts from the same host. So far, these non-pathogenic isolates were overlooked due to their less economic importance and lack of genomic information. We have carried out detailed ecological and evolutionary study focusing on diverse lifestyles of these strains. Phylogenomic analysis revealed two major lineages corresponding to X. sontii (ML-I) and X. oryzae (ML-II) species. Interestingly, one of the non-pathogenic Xanthomonas strains belonging to X. maliensis is intermediary to both the major lineages/species suggesting on-going diversification and selection. Accordingly, pangenome analysis revealed large number of lifestyle specific genes with atypical GC content indicating role of horizontal gene transfer in genome diversification. Our comprehensive comparative genomic investigation of major lineages has revealed that impact of recombination is more for X. sontii as compared to X. oryzae. Acquisition of type III secretion system and its effectome along with a type VI secretion system also seem to have played a major role in the pathogenic lineage. Other known key pathogenicity clusters or genes like biofilm forming cluster, cellobiohydrolase and non-fimbrial adhesin (yapH) are exclusive to pathogenic lineage. However, commonality of loci encoding exopolysacharide, rpf signalling molecule, iron-uptake, xanthomonadin pigment, etc. suggests their essentiality in host adaptation. Overall, this study reveals evolutionary history of pathogenic and non-pathogenic strains and will further open up a new avenue for better management of pathogenic strains for sustainable cultivation of a major staple food crop.

evolutionary biology↗

bioRxiv2015

Species range expansion constrains the ecological niches of resident butterflies.

AimChanges in community composition resulting from environmental changes modify biotic interactions and affect the distribution and density of local populations. Such changes are currently occurring in nettle-feeding butterflies in Sweden where Araschnia levana has recently expanded its range northward and is now likely to interact with the resident species (Aglais urticae and Aglais io). Butterfly occurrence data collected over years and across regions enabled us to investigate how a recent range expansion of A. levana may have affected the environmental niche of resident species.\n\nLocationWe focused on two regions of Sweden (Sk[a]ne and Norrstrom) where A. levana has and has not established, and two time-periods (2001-2006, 2009-2012) during its establishment in Sk[a]ne.\n\nMethodsWe performed two distinct analyses in each region using the PCA-env and the framework described in Broennimann et al. (2012). First, we described the main sources of variation in the environment. Second, in each time-period and region, we characterized the realized niches of our focal species across topographic and land use gradients. Third, we quantified overlaps and differences in realized niches between and within species over time.\n\nResultsIn Sk[a]ne, A. levana has stabilized its distribution over time while the distribution of the native species has shifted. These shifts depicted a consistent pattern of avoiding overlap between the native species and the environmental space occupied by A. levana, and it was stronger for A. urticae than for A. io. In both regions, we also found evidence of niche partitioning between native species.\n\nMain conclusionsInterspecific interactions are likely to affect local species distributions. It appears that the ongoing establishment of A. levana has modified local biotic interactions, and induced shifts in resident species distributions. Among the mechanisms that can explain such patterns of niche partitioning, parasitoid-driven apparent competition may play an important role in this community.

Ecology↗

bioRxiv2016

Ecological factors rather than barriers to dispersal shape genetic structure of algal symbionts in horizontally-transmitting corals

Many reef-building corals acquire their algal symbionts (Symbiodinium sp.) from the local environment upon recruitment. This horizontal transmission strategy where hosts pair with locally available symbionts could serve to increase coral fitness across diverse environments, as long as hosts maintain high promiscuity and symbionts adapt locally. Here, we tested this hypothesis in two coral species by comparing host and symbiont genetic structures across different spatial scales in Micronesia. Each host species associated with two genetically distinct Symbiodinium lineages, confirming high promiscuity in broadly dispersing hosts. However, contrary to our initial expectation, symbiont genetic structure was independent of physical barriers to dispersal between islands, unlike genetic structure of their hosts that was nearly perfectly explained by ocean currents. Instead, Symbiodinium consistently demonstrated genetic divergence among local reefs and between the two host species at each island, although not necessarily between distant islands. These observations indicate that Symbiodinium lineages disperse much more broadly than previously thought and continuously adapt to specific hosts and reef environments across their range, following the classical Baas Beckings hypothesis: \"Everything is everywhere, but the environment selects\". Overall, our findings confirm that horizontal transmission could be a mechanism for broadly dispersing coral species to enhance their local fitness by associating with locally adapted symbionts. Dramatic differences in factors driving the genetic structures of horizontally-transmitting corals and their Symbiodinium imply that viewing their combined genomes as a single entity ( hologenome) would not be useful in the context of their evolution and adaptation.

Ecology↗

bioRxiv2016

Correlation/causation in ecology: towards mechanistic explanations for the Species-Area Relationship

There is a common intuition in biology that strict laws are very difficult to be found. Still, there are recurrent patterns in nature, suggesting broad generalizations and understanding of phenomena. The problem is that many generalizations in biology, especially in the form of correlations, might be decoupled from causality, weakening their power of explanation. Here, I bring an example on the Species-Area Relationship (SAR). The SAR is a well-known generalization in biology. The recurrent pattern states a positive relationship between area size and species richness. Understanding the mechanisms why there is a correlation between area and diversity remains a major challenge. I suggest an explicitly focus on mechanistic explanations for the SAR. I propose to use the integration, comparison and interpretation of other (associated or secondary) natural patterns in the searching for causal explanations. Area per se might not account for causality in species diversification or absolute species richness in larger regions. Biotic and abiotic factors of a given area might be studied in order to discover the causal underpinnings of the SAR.

Ecology↗

bioRxiv2016

Remotely-sensed tornado signatures indicate an ecological threshold for eagle nest destruction

Bald Eagles (Haliaeetus leucocephalus) will reuse massive nests placed high in trees over multiple years, potentially exposing them to catastrophe loss during severe storms. The stochasticity of localized weather, however, has traditionally been viewed as impeding the quantitative study of such risks. In March 2015 a severe weather outbreak along the Arkansas River near Tulsa, Oklahoma caused widespread damage among a highly-concentrated and long-monitored population of nesting Bald Eagles. We conducted field surveys on the extent of nest loss and consulted weather and observer records to determine what characteristics of the storm (maximum azimuthal wind shear) or nests (years of use) might have been associated with nest destruction. We found 5 of 9 nests along a ~24km stretch of the river were destroyed during the storm, causing the death of at least 8 eaglets. Mean years of use was higher among destroyed nests (4.8) than surviving nests (4.0), though not significantly so within this limited sample. The degree of maximum azimuthal shear (i.e., wind rotation) during the storm within 800m of the nests, however, did significantly differ both in terms of maximums (15.8 vs 9.5 ms-1) and means (9.4 vs 6.6 ms-1) for destroyed versus persisting nests, respectively. Our findings suggest a threshold of tornadic wind shear beyond which Bald Eagle nests, irrespective of age, could be prone to catastrophe. Such insights are key to developing accurate models of population persistence, especially in light of potential shifts in severe weather patterns under various climate change scenarios.

Ecology↗