Negative Co-occurrence Patterns Research Articles

Examining the relative influence of dispersal and competition on co-occurrence and functional trait patterns in response to disturbance

Disturbance gradients are particularly useful for understanding the relative influences of competition and dispersal. Shortly after disturbance, plant composition should be influenced more strongly by dispersal than competition; over time, this should reverse, with competition becoming more important. As such, we predicted that plant functional traits associated with high dispersal ability would be over-represented shortly after a disturbance event occurs, while those associated with high competitive ability would have increased representation as time progresses. Additionally, it has been suggested that competitive interactions may contribute to negative co-occurrence patterns; if this is the case, negative co-occurrence patterns should also increase as time-since-disturbance increases. Here, we examine how functional trait and co-occurrence patterns change over time following a herbicide-based disturbance, compared to undisturbed vegetation, in a temperate, old-field grassland dominated by herbaceous perennials. In our study system, negative co-occurrence patterns were most pronounced in disturbed plots one year after herbicide application, consistent with several lines of evidence that dispersal can strongly impact both composition and co-occurrence patterns. Over three years post-disturbance, co-occurrence patterns in disturbed plots decreased, becoming more similar to control plots. This pattern is inconsistent with the expectation that competition contributes to negative co-occurrence patterns, at least over three growing seasons. More pronounced negative co-occurrence patterns were associated with higher species evenness among plots. Functional traits related to increased dispersal (mean seed mass, and proportion of stoloniferous/rhizomatous species) and competitive ability (mean species height, and mean specific leaf area) did not differ significantly across treatments, with the exception of mean height in the third-year post-disturbance; however, the overall trajectory of this trait was inconsistent with theoretical expectations. Overall, co-occurrence patterns changed across the gradient of time-since disturbance, but not as expected; functional trait patterns (trait means, functional diversity measures) were not responsive to our experimental disturbance gradient.

High Dietary Niche Overlap Between Non-native and Native Ant Species in Natural Ecosystems.

Ants represent a highly diverse and ecologically important group of insects found in almost all terrestrial ecosystems. A subset of ant species have been widely transported around the globe and invade many natural ecosystems, often out-competing native counterparts and causing varying impacts on recipient ecosystems. Decisions to control non-native ant populations require an understanding of their interactions and related impacts on native communities. We employed stable isotope analysis and metabarcoding techniques to identify potential dietary niche overlap and identify gut contents of 10 ant species found in natural ecosystems in Aotearoa New Zealand. Additionally, we looked at co-occurrence to identify potential competitive interactions among native and non-native ant species. Ants fed mainly across two trophic levels, with high dietary overlap. Relative to other ant species sampled, two non-native ant species, Linepithema humile and Technomyrmex jocosus, were found to feed at the lowest trophic level. The largest isotopic niche overlap was observed between the native Monomorium antarcticum and the invasive Ochetellus glaber, with analyses revealing a negative co-occurrence pattern. Sequence data of ant gut content identified 51 molecular operational taxonomic units, representing 22 orders and 34 families, and primarily consisting of arthropod DNA. Although we generally found high dietary overlap among species, negative occurrence between a dominant, non-native species and a ubiquitous native species indicates that species-specific interactions could be negatively impacting native ecosystems. Our research progresses and informs the currently limited knowledge around establishing protocols for metabarcoding to investigate ant diet and interactions between native and non-native ant species.

Gut-derived Flavonifractor species variants are differentially enriched during in vitro incubation with quercetin

Flavonoids are a common component of the human diet with widely reported health-promoting properties. The gut microbiota transforms these compounds affecting the overall metabolic outcome of flavonoid consumption. Flavonoid-degrading bacteria are often studied in pure and mixed cultures but the multiple interactions between quercetin-degraders and the rest of the community have been overlooked. In this study, a comparative metataxonomic analysis of fecal communities supplemented with the flavonoid quercetin led us to identify a potential competitive exclusion interaction between two sequence variants related to the flavonoid-degrading species, Flavonifractor plautii, that belong to the same genus but different species. During incubation of fecal slurries with quercetin, the relative abundance of these two variants was inversely correlated; one variant, ASV_65f4, increased in relative abundance in half of the libraries and the other variant, ASV_a45d, in the other half. This pattern was also observed with 6 additional fecal samples that were transplanted into germ-free mice fed two different diets. Mouse’s diet did not change the pattern of dominance of either variant, and initial relative abundances did not predict which one ended up dominating. Potential distinct metabolic capabilities of these two Flavonifractor-related species were evidenced, as only one variant, ASV_65f4, became consistently enriched in complex communities supplemented with acetate but without quercetin. Genomic comparison analysis of the close relatives of each variant revealed that ASV_65f4 may be an efficient utilizer of ethanolamine which is formed from the phospholipid phosphatidylethanolamine that is abundant in the gut and feces. Other discordant features between ASV_65f4- and ASV_a45d-related groups may be the presence of flagellar and galactose-utilization genes, respectively. Overall, we showed that the Flavonifractor genus harbors variants that present a pattern of negative co-occurrence and that may have different metabolic and morphological traits, whether these differences affect the dynamic of quercetin degradation warrants further investigation.

Year-round passive acoustic data reveal spatio-temporal patterns in marine mammal community composition in the Weddell Sea, Antarctica

To date, the majority of studies investigating marine mammal distribution and behavior take a single-species perspective, which is often driven by the logistic difficulties of collecting appropriate data at sea. Passive acoustic monitoring, provided recording tools exhibit sufficient bandwidth, has the potential to provide insights into community structure as devices operate autonomously simultaneously collecting data on baleen, pinniped and toothed whale acoustic presence. Data can provide information on local species diversity, residency times and co-occurrence. Here, we used multi-year passive acoustic data from 6 sites in the Weddell Sea, Southern Ocean, to explore how local marine mammal community compositions develop over time and in relation to sea-ice. Diversity peaked in austral late spring and early summer, shortly before seasonal sea-ice break-up. The effective number of species exhibited little variation over time, reflecting that species remain in Antarctic waters throughout austral winter. Community composition showed almost complete seasonal overturn, indicating that species replace each other throughout the year. For all 6 sites, community dissimilarity increased with increasing temporal distance, reflecting temporal trends in community composition beyond seasonality. Several species exhibited significant positive or negative co-occurrence patterns over time. These seasonal associations were consistent across all 5 oceanic sites, but partly inversed at the Western Antarctic Peninsula recording site. This study shows that the application of biodiversity metrics to passive acoustic monitoring data can foster insights into the timing of behaviors and community composition, which can boost the interpretation of responses in the light of ongoing environmental changes.

Good neighbors aplenty: fungal endophytes rarely exhibit competitive exclusion patterns across a span of woody habitats.

Environmental forces and biotic interactions, both positive and negative, structure ecological communities, but their relative roles remain obscure despite strong theory. For instance, ecologically similar species, based on the principle of limiting similarity, are expected to be most competitive and show negative interactions. Specious communities that assemble along broad environmental gradients afford the most power to test theory, but the communities often are difficult to quantify. Microbes, specifically fungal endophytes of wood, are especially suited for testing community assembly theory because they are relatively easy to sample across a comprehensive range of environmental space with clear axes of variation. Moreover, endophytes mediate key forest carbon cycle processes, and although saprophytic fungi from dead wood typically compete, endophytic fungi in living wood may enhance success through cooperative symbioses. To classify interactions within endophyte communities, we analyzed fungal DNA barcode variation across 22 woody plant species growing in woodlands near Richmond, New South Wales, Australia. We estimated the response of endophytes to the measured wood environment (i.e., 11 anatomical and chemical wood traits) and each other using latent-variable models and identified recurrent communities across wood environments using model-based classification. We used this information to evaluate whether (1) co-occurrence patterns are consistent with strong competitive exclusion, and (2) a priori classifications by trophic mode and phylum distinguish taxa that are more likely to have positive vs. negative associations under the principle of limiting similarity. Fungal endophytes were diverse (mean=140 taxa/sample), with differences in community composition structured by wood traits. Variation in wood water content and carbon concentration were associated with especially large community shifts. Surprisingly, after accounting for wood traits, fungal species were stillmore than three timesmore likely to have positive than negative co-occurrence patterns. That is, patterns consistent with strong competitive exclusion were rare, and positive interactions among fungal endophytes were more common than expected. Confirming the frequency of positive vs. negative interactions among fungal taxa requires experimental tests, and our findings establish clear paths for further study. Evidence to date intriguingly suggests that, across a wide range of wood traits, cooperation may outweigh combat for these fungi.

Habitat filtering of six coexisting Heliconia species in a lowland tropical rain forest in Amazonian Ecuador

AbstractHerbaceous plants are often under-studied in tropical forests, despite their high density and diversity, and little is known about the factors that influence their distribution at microscales. In a 25-ha plot in lowland Amazonian rain forest in Yasuní National Park, Ecuador, we censused six species of Heliconia (Heliconiaceae) in a stratified random manner across three topographic habitat types. We observed distribution patterns consistent with habitat filtering. Overall, more individuals occurred in the valley (N = 979) and slope (N = 847) compared with the ridge (N = 571) habitat. At the species level, Heliconia stricta (N = 1135), H. spathocircinata (N = 309) and H. ortotricha (N = 36) all had higher abundance in the valley and slope than ridge. Further, H. vellerigera (N = 20) was completely absent from the ridge. Conversely, H. velutina (N = 903) was most common in the drier ridge habitat. The two most common species (H. stricta and H. velutina) had a reciprocal or negative co-occurrence pattern and occurred preferentially in valley versus ridge habitats. These results suggest that taxa within this family have different adaptations to the wetter valley versus the drier ridge and that habitat partitioning contributes to coexistence.

Co-occurrence patterns between plant-parasitic nematodes and arbuscular mycorrhizal fungi are driven by environmental factors

The relationships between co-occurrence patterns of plant-parasitic nematodes and arbuscular mycorrhizal fungus (AMFs) are not fully understood. Few field studies assess co-occurrence patterns, evidencing the lack of information on soil-limiting conditions for favorable management of AMFs. The aim was therefore to evaluate co-occurrence patterns between plant-parasitic nematodes and AMFs and the probable environmental conditions that were associated to these patterns. We sampled three sites in each of ten fields and collected an abundance of nematodes and AMF spores and physical-chemical soil data. We evaluated co-occurrence patterns using combinations between nematodes and AMFs in both samplings (soil and roots) through probabilistic models. We also performed a redundancy analysis to evaluate which environmental variables were correlated to negative and positive patterns found between both groups. Plant-parasitic nematodes and AMFs showed negative co-occurrence patterns on the root-rhizospheric soil interface as a result of the competition. In the soil, the groups showed an apparent differentiation of niche, and the competition occurs within each group. Soil variation, mainly on alterations of potassium, phosphorus and moisture are the main characteristics that are associated to changes in the assemblages of these groups. Co-occurrence patterns indicated in the present study show an important pathway to conservative management of the soil and improvement of the crop growth in agricultural landscapes.

Effect of Long-term Oil Contamination on the Microbial Molecular Ecological Networks in Saline-alkali soils

Long-term oil contamination alters the structures of soil microbial communities, as well as decreases the community diversity, posing a great threat to the ecosystem. To determine the possible influence of long-term oil contamination on microbial interactions in saline-alkali soils, microbial functional molecular ecological networks were studied in both contaminated and uncontaminated soils from Shengli oil field by constructing random networks based on null model. The results demonstrated that the overall networks were significantly different between contaminated and uncontaminated soils (P<0.001). Network size, links, average connectivity, modules and modularity were all decreased in soil with oil contamination, indicating that oil contamination altered the topological structure of microbial functional molecular ecological network. Module hub and connectors were different in contaminated and uncontaminated soils. The topological roles of the genes (module hub and connectors) were altered by oil contamination. Sub-networks of genes involved in alkane and polycyclic aromatic hydrocarbon degradation were also constructed. Negative co-occurrence patterns prevailed among functional genes, thereby indicating probable competition relationships among functional groups.

Long-Term Oil Contamination Alters the Molecular Ecological Networks of Soil Microbial Functional Genes

With knowledge on microbial composition and diversity, investigation of within-community interactions is a further step to elucidate microbial ecological functions, such as the biodegradation of hazardous contaminants. In this work, microbial functional molecular ecological networks were studied in both contaminated and uncontaminated soils to determine the possible influences of oil contamination on microbial interactions and potential functions. Soil samples were obtained from an oil-exploring site located in South China, and the microbial functional genes were analyzed with GeoChip, a high-throughput functional microarray. By building random networks based on null model, we demonstrated that overall network structures and properties were significantly different between contaminated and uncontaminated soils (P < 0.001). Network connectivity, module numbers, and modularity were all reduced with contamination. Moreover, the topological roles of the genes (module hub and connectors) were altered with oil contamination. Subnetworks of genes involved in alkane and polycyclic aromatic hydrocarbon degradation were also constructed. Negative co-occurrence patterns prevailed among functional genes, thereby indicating probable competition relationships. The potential “keystone” genes, defined as either “hubs” or genes with highest connectivities in the network, were further identified. The network constructed in this study predicted the potential effects of anthropogenic contamination on microbial community co-occurrence interactions.

Using direct amplification and next-generation sequencing technology to explore foliar endophyte communities in experimentally inoculated western white pines

Abstract Fungal endophytes can influence survivability and disease severity of trees. Here we characterized the endophyte community in Pinus monticola (western white pine), an important species in the northwest USA, largely decimated by pathogenic fungi. We also assessed the ability to successfully inoculate seedlings with desirable endophytes, with the long-term goal of providing a protective microbiome and added defense from pathogens. P. monticola seedlings were inoculated in the field with potential pathogen antagonists and fungi isolated from healthy mature trees. Following inoculations direct amplification and next generation sequencing were used to characterize fungal endophyte communities, and explore interspecific competition, diversity, and co-occurrence patterns in needle tissues. Negative co-occurrence patterns between inoculated fungi and potential pathogens, as well as many other species, suggest early competitive interactions. Our study explores early endophyte community assemblage and shows that fungal inoculations may influence tree growth.

Dispersal strength influences zooplankton co-occurrence patterns in experimental mesocosms.

Negative co-occurrence patterns are intriguing because they may reflect the outcome of interspecific interactions and therefore signal how competition shapes communities. However, other factors also contribute to these patterns. For example, theoretical studies as well as two survey-based studies have all suggested that dispersal may also impact these patterns. While natural communities commonly have nonrandom patterns of negative co-occurrence, understanding how different processes drive these patterns requires further research. We tested the influence of dispersal on co-occurrence patterns using a zooplankton mesocosm experiment with four different dispersal treatments varying in the number of dispersers delivered into mesocosms on regular intervals. Our dispersal treatments were intended to adjust the relative importance of dispersal and competition experienced within mesocosms (i.e., high dispersal results in a relatively low influence of competition on species composition and vice versa). Higher dispersal translated into increased zooplankton species richness and inter-mesocosm compositional similarity, and also changed species occupancy patterns such that species occurrences were more even across mesocosms in higher-dispersal treatments. Dispersal treatments also differed markedly in species co-occurrence patterns. Negative co-occurrence patterns were significant for all but the lowest-dispersal treatment, peaked in the intermediate-dispersal treatments, and declined in the highest-dispersal treatment. Stability analyses illustrate that co-occurrence differences are robust to the exclusion of any single mesocosm in null model analyses. Dispersal treatments did not significantly differ with respect to abiotic variation, which has been recognized as a potential driver of negative co-occurrence patterns. These results suggest that not only can dispersal influence patterns of negative co-occurrence via changes to species richness and distribution (occupancy patterns among mesocosms), but the degree to which they do so varies nonlinearly with the strength of dispersal. Critically, because negative co-occurrence patterns were nonsignificant when the contribution of dispersal was lowest, it is possible that dispersal contributes strongly to many observed patterns of negative co-occurrence. Consequently, great care should be taken prior to interpreting significant co-occurrence tests as a product of species interactions.

Species richness and meta-community structure of land snails along an altitudinal gradient on Bioko Island, Equatorial Guinea

We investigated the land-snail fauna of rain forests on the eastern slopes of Pico Biao on Bioko Island in the Gulf of Guinea. Thirty-seven plots were studied along an altitudinal transect reaching from sea level (lowland rain forest) to an altitude of 1,830 m (mossy forest). A total of 1,755 specimens were collected and were assigned to 68 land-snail species. Eleven species were new records for Bioko. At least 15 of the recorded species are endemic to Bioko. The degree of endemism was high in mossy forest (23%) and in lowland rain forest (20%), but lower in montane forest (8%). Species richness showed a hump-shaped distribution along the altitudinal gradient with a maximum at 500 m a.s.l. Species richness peaked in forests in which there had been selective logging more than 50 years ago, indicating that some disturbance may have beneficial effects on biodiversity. Species richness was correlated with the thickness of leaf litter. The availability and quality of suitable microhabitats is more important for the occurrence of snail species than gradients of otherwise often decisive environmental parameters like temperature, which are strongly correlated with altitude. A lack of clustering of the occurrences of different snail species along the altitudinal gradient indicated a Gleasonian meta-community structure with individualistic responses of the various species to environmental parameters. No negative co-occurrence patterns that might provide evidence for interspecific competition could be detected. The frequent coexistence of morphologically similar, and presumably ecologically equivalent, congeneric species may indicate that such equivalents do not exclude each other as predicted by the neutral theory of biodiversity. However, current knowledge about individual snail species is too scanty to exclude the possibility that niches of congeneric species differ in some details.

Spatial, Environmental, and Biotic Determinants of Zooplankton Community Composition in Subarctic Lakes and Ponds in Wapusk National Park, Canada

Northern regions are expected to experience large environmental change over the next few decades. The response of biota will depend on changes in the local environment, regional processes that influence lake connectivity, and species interactions. In 2008, we surveyed 92 lakes and ponds across Wapusk National Park, located on the southwestern shore of Hudson Bay. At each site we assessed water chemistry and zooplankton community composition. In an effort to understand how the aquatic ecosystems will respond to future environmental change, we determined local characteristics (e.g., water chemistry), regional spatial factors (e.g., dispersal), and biotic interactions (e.g., species associations) influencing community composition. Important environmental variables included lake area, pH, ionic composition, total phosphorus, and chlorophyll a; however, spatial variables explained more variation than environmental variables, suggesting that dispersal is an important driver of zooplankton composition in this region. Additionally, species exhibited negative co-occurrence patterns, suggesting biotic interactions are important in structuring the zooplankton communities. As environmental conditions change and the distribution of habitat (i.e., coastal fen, interior peatland, and spruce forest) shifts, evidence that the park’s zooplankton community is spatially structured coupled with our suspicion that zooplankton are likely to experience high dispersal levels in Wapusk leads us to suggest zooplankton may indeed be able to track changing environmental conditions within the park, although it remains unclear how species interactions will modify this expectation.

Avian succession along ecological gradients: Insight from species-poor and species-rich communities of Sylvia warblers

Abstract The mechanisms responsible for species replacement during ecological successions is a long-standing and open debate. In this study, we examined the distribution of the Sardinian warbler Sylvia melanocephala along two grassland-to-forest gradients, one in a high-diversity area (Albera-Aspres chain in Catalonia: eight Sylvia warbler species) and one in a low-diversity area (Mount Hymittos in Greece: four species). In Catalonia, distribution models suggested that the apparent exclusion of S. melanocephala from the open and forest ends of the gradient may be explained entirely by the preference of S. melanocephala for mid-successional shrublands. However, a joint analysis of both data sets revealed that: 1) S. melanocephala was more evenly distributed along the vegetation gradient in Greece, suggesting ecological release in the low-diversity area; and 2) a distribution model assuming interspecific competition (based on the distribution of Sylvia species showing a negative co-occurrence pattern with S. melanocephala) had a significantly higher predictive ability than a distribution model based on habitat variables alone. Our study supports the view that species turnover along ecological gradients generally results from a combination of intrinsic preferences and interspecific competition.

Liana co-occurrence patterns in a temperate rainforest

Questions: Are liana–host interactions structured at the community level? Do liana–host interactions differ between species, growth form guilds or habitats? Location: Otari-Wilton's Bush, on the southern tip of North Island, New Zealand. The forest contains 75 ha of mature and regenerating conifer–broadleaf forest. Methods: Nine liana species were quantified among 217 trees to test for negative co-occurrence patterns. We also conducted additional analyses within and among compartments embedded in the community-level matrix. Liana and host abundance distributions were assessed across two contrasting habitats. Results: Community-level analyses revealed negative co-occurrence patterns. Positive, neutral and negative co-occurrence patterns were found among compartments within the community-level matrix. Host species compartments were consistent with randomized expectations, while positive co-occurrence patterns were found within the host species matrix. Negative co-occurrence patterns were found inconsistently among lianas that share the same region of host space, and those that do not. Conclusions: Overall, results indicate the liana community is structured non-randomly. Liana–host interactions appear to follow an opportunistic growth strategy and interactions are due mostly to habitat partitioning.

A hierarchical framework for investigating epiphyte assemblages: networks, meta‐communities, and scale

Epiphytes are an important component of many forested ecosystems, yet our understanding of epiphyte communities lags far behind that of terrestrial-based plant communities. This discrepancy is exacerbated by the lack of a theoretical context to assess patterns in epiphyte community structure. We attempt to fill this gap by developing an analytical framework to investigate epiphyte assemblages, which we then apply to a data set on epiphyte distributions in a Panamanian rain forest. On a coarse scale, interactions between epiphyte species and host tree species can be viewed as bipartite networks, similar to pollination and seed dispersal networks. On a finer scale, epiphyte communities on individual host trees can be viewed as meta-communities, or suites of local epiphyte communities connected by dispersal. Similar analytical tools are typically employed to investigate species interaction networks and meta-communities, thus providing a unified analytical framework to investigate coarse-scale (network) and fine-scale (meta-community) patterns in epiphyte distributions. Coarse-scale analysis of the Panamanian data set showed that most epiphyte species interacted with fewer host species than expected by chance. Fine-scale analyses showed that epiphyte species richness on individual trees was lower than null model expectations. Therefore, epiphyte distributions were clumped at both scales, perhaps as a result of dispersal limitations. Scale-dependent patterns in epiphyte species composition were observed. Epiphyte-host networks showed evidence of negative co-occurrence patterns, which could arise from adaptations among epiphyte species to avoid competition for host species, while most epiphyte meta-communities were distributed at random. Application of our "meta-network" analytical framework in other locales may help to identify general patterns in the structure of epiphyte assemblages and their variation in space and time.

Network properties of arboreal plants: Are epiphytes, mistletoes and lianas structured similarly?

Network analyses provide a unified framework to evaluate different types of species interactions. We used a network approach to comparatively evaluate three types of arboreal plant metacommunities. Interactions between mistletoes, lianas and epiphytes and their host trees were quantified in two New Zealand forests and individual-based null models were used to test for non-random patterns in network degree, nestedness and negative co-occurrence patterns. Arboreal plants were simulated to randomly occur on individual host trees to derive ‘null’ interaction matrices, which were then compared to the observed matrix. Results showed that mistletoes, lianas and epiphytes had very different network properties. Mistletoe and liana degree distributions exhibited fewer links than expected under the null model, indicating strong host preferences. Conversely, degree distributions for epiphytes were consistent with randomised expectations. Mistletoes and lianas were less nested than null model expectations and instead showed support for negative co-occurrence patterns, meaning mistletoe and liana species tended to have mutually exclusive host preferences. Conversely, epiphytes were more nested than expected by chance and showed positive co-occurrence patterns. Overall results indicate that plant–plant interactions exhibited by different types of arboreal plants have very different network properties. We hypothesize that these differences result from (1) differences in coevolutionary dynamics between arboreal plants and their hosts, which range from parasitic (mistletoes) to commensal (epiphytes), and (2) biotic interactions among arboreal plant species for access to host trees.

Null model tests of clustering of species, negative co-occurrence patterns and nestedness in meta-communities

Null model tests of clustering of species, negative co-occurrence patterns and nestedness in meta-communities