Dissimilarity In Community Composition Research Articles

Linking abundance and community of microbial N2O-producers and N2O-reducers with enzymatic N2O production potential in a riparian zone

As aquatic-terrestrial ecotones, riparian zones are hotspots not only for denitrification but also for nitrous oxide (N2O) emission. Due to the potential role of nosZ II in N2O mitigation, emerging studies in terrestrial ecosystems have taken this newly reported N2O-reducer into account. However, our knowledge about the interactions between denitrification activities and both N2O-producers and reducers (especially for nosZ II) in aquatic ecosystems remains limited. In this study, we investigated spatiotemporal distributions of in situ N2O flux, potential N2O production rate, and potential denitrification rate, as well as of the related genes in a riparian zone of Baiyangdian Lake. Real-time quantitative PCR (qPCR) and high-throughput sequencing targeted functional genes were used to analyze the denitrifier communities. Results showed that great differences in microbial activities and abundances were observed between sites and seasons. Waterward sediments (constantly flooded area) had the lowest N2O production potential in both seasons. Not only the environmental factors (moisture content, NH4+ content and TOM) but also the community structure of N2O-producers and N2O-reducers (nirK/nirS and nosZ II/nosZ I ratios) could affect the potential N2O production rate. The abundance of the four functional genes in the winter was higher than in the summer, and the values all peaked at the occasionally flooded area in the winter. The dissimilarity in community composition was mainly driven by moisture content. Altogether, we propose that the N2O production potential was largely regulated by the community structure of N2O-producers and N2O-reducers in riparian zones. Increasing the constantly flooded area and reducing the occasionally flooded area of lake ecosystems may help reduce the level of denitrifier-produced N2O.

Polypore Communities and Their Substrate Characteristics in Atlantic Forest Fragments in Southeast Brazil

Anthropogenic environmental changes have resulted in biodiversity crisis. Although tropical rainforests are one of the global biodiversity hotspots, their biodiversity is still poorly known. Especially fungi are poorly represented in national Red Lists and conservation plans, despite their important role in ecosystem functioning. We studied wood-inhabiting fungi (polypores) in four areas within two Atlantic rainforest fragments in Southeast Brazil. Our aim was to investigate fungal substrate characteristics and community composition. Deadwood amount ranged from 27 to 82 m3/ha among the four study areas and altogether we recorded 53 polypore species. More species were observed in intermediate and late decay stages than in early decay stages, but other deadwood variables did not explain the occurrence of polypores. Similarity in polypore community composition within and among the areas was low. Dissimilarity originated mostly from species turnover from a transect and area to another, and no nestedness in species occurrence pattern was detected. Hence, the observed dissimilarity in community composition was probably a result of heterogeneity in forest composition and structure, instead of environmental gradients or substrate limitations. These results corroborate previous polypore studies from the Atlantic forest in that tropical polypores are specialists toward particular decay stages. To develop ecologically effective conservation program for tropical polypores, more studies are needed on their distribution and abundance globally.

Tropical Estuarine Macrobenthic Communities Are Structured by Turnover Rather than Nestedness.

Turnover (i.e., species substitution) and nestedness (i.e., subsets of species from more diverse locations), the two main mechanisms used to explain the beta diversity of biological communities, have different implications for biodiversity conservation. To better understand how these mechanisms contribute to beta diversity, we tested the following hypotheses: (i) greater dissimilarity in community composition occurs between estuarine zones than other hierarchical level studied; (ii) beta diversity in these communities develops by turnover in estuaries with a lower degree of anthropogenic impact, but by nestedness in estuaries with a greater degree of anthropogenic impact; and (iii) the structuring mechanism is independent of season. We studied two tropical estuaries (dry and wet seasons) that vary in terms of land-use of the drainage basins. Subtidal benthic macroinvertebrates were sampled along the estuarine gradient in each of the two estuaries. The additive partitioning approach to species diversity was used to determine the hierarchical scale with the greatest dissimilarity in community composition. General beta diversity was measured using the Sorensen dissimilarity index, partitioning the turnover and nestedness components. The greatest dissimilarity in the composition of the communities occurred between the zones along the estuarine gradient in both seasons (dry = 58.6%; wet = 46.3%). In the estuary with a lower degree of anthropogenic influence, benthic macroinvertebrate diversity was generated by turnover regardless of the season. In the estuary with a greater degree of anthropogenic impact, beta diversity was structured by turnover during the dry season and a combination of both mechanisms during the wet season. We conclude that turnover is the principal mechanism responsible for beta diversity in benthic macroinvertebrate communities in tropical estuaries.

Skin fungal community and its correlation with bacterial community of urban Chinese individuals.

BackgroundHigh-throughput sequencing has led to increased insights into the human skin microbiome. Currently, the majority of skin microbiome investigations are limited to characterizing prokaryotic communities, and our understanding of the skin fungal community (mycobiome) is limited, more so for cohorts outside of the western hemisphere. Here, the skin mycobiome across healthy Chinese individuals in Hong Kong are characterized.ResultsBased on a curated fungal reference database designed for skin mycobiome analyses, previously documented common skin colonizers are also abundant and prevalent in this cohort. However, genera associated with local terrains, food, and medicine are also detected. Fungal community composition shows interpersonal (Bray-Curtis ANOSIM = 0.398) and household (Bray-Curtis ANOSIM = 0.134) clustering. Roles of gender and age on diversity analyses are test- and site-specific, and, contrary to bacteria, the effect of household on fungal community composition dissimilarity between samples is insignificant. Site-specific, cross-domain positive and negative correlations at both community and operational taxonomic unit levels may uncover potential relationships between fungi and bacteria on skin.ConclusionsThe studied Chinese population presents similar major fungal skin colonizers that are also common in western populations, but local outdoor environments and lifestyles may also contribute to mycobiomes of specific cohorts. Cohabitation plays an insignificant role in shaping mycobiome differences between individuals in this cohort. Increased understanding of fungal communities of non-western cohorts will contribute to understanding the size of the global skin pan-mycobiome, which will ultimately help understand relationships between environmental exposures, microbial populations, and the health of global humans.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-016-0192-z) contains supplementary material, which is available to authorized users.

A comparative study of oribatid mite communities in red wood ant Formica polyctena nests and surrounding soil in a Finnish oak forest

Abstract Ant nests are also inhabited by other invertebrates, ant associates. The oribatid mite (Acari: Oribatida) fauna of nests is poorly known, both in terms of abundance and diversity. We compared the oribatid assemblages within and outside red wood ant Formica polyctena nests in a Finnish oak forest. Altogether ten mounds were investigated and comparable samples were collected from adjacent soil 4 m from each mound. A total of 10 529 specimens were recovered, 4959 of them in mounds and 5633 in soil. The specimens represented 74 species (and two higher taxa) belonging to 60 genera and 39 families. Significant differences in abundance or diversity were not observed between nests and soil habitats. For nest samples the abundance of specimens significantly correlated with diversity indicating that mounds form rich habitat patches with a diverse set of niches. Mound size had no effect on community composition. The nest and soil habitats were predominantly occupied by different species resulting in dissimilarities in community composition; 34% of the species showed a preference for nest habitat and 50% for soil habitats, whereas16% were indifferent with equal abundances in both habitats. Nonetheless, most of the species with a preference for nests are frequently found in various habitats in nature, and may be classified as facultative myrmecophiles that maintain populations also in ant nests. Ant nests host abundant and diverse oribatid assemblages, which differ from the fauna in adjacent soil, and wood ants are therefore important factors in maintaining biodiversity.

Resilience of a phytoplankton community after disturbance in a subtropical reservoir: A case study in Feitsui Reservoir, Taiwan

Feitsui Reservoir (FTR), a subtropical, dammed water reservoir located in Taipei, Taiwan was constructed in 1986 to supply drinking water to the Taipei metropolitan area. During 1996–2005, highway construction in the watershed was associated with the input of anthropogenic pollutants into the FTR and caused a significant alteration in water quality and increased eutrophication of the FTR. The present study was performed to analyze the resilience of the phytoplankton community and to determine the indicators of trophic change. Analysis with multidimensional scaling of the similarity in community composition showed that the abundance of various phytoplankton taxa changed during the disturbance and did not return to the pre-disturbance state. An alteration in the dominance of phytoplankton assemblages occurred between cyanobacteria and green algae. The main species contributing to the dissimilarity in community composition between pre-disturbance, during disturbance, and post-disturbance were Microcystis, Aphanocapsa, and desmids. The factors driving such alterations were organic and dissolved ionic substances, which were due to domestic wastes and runoff from the construction site, respectively. This study provides evidence that this monomictic water body was strongly affected by the turnover time of turbid pollutants stored in the hypolimnion and thus the recovery time of the aquatic community. During resilience, the reduction in phytoplankton density, increased abundance of desmids and chrysophytes, and elevated diversity indices were good indicators of oligotrophication in the FTR. In order to lower the effects of disturbance, on-site treatment with a wetland is considered the best management practice.

Plant Community Response Following Removal of Juniperus virginiana from Tallgrass Prairie: Testing for Restoration Limitations

Woody plant encroachment in natural grasslands is a widely documented global phenomenon that alters ecosystem dynamics by altering historic vegetation composition and suppressing herbaceous productivity. Abundant woody plants often suppress native plants sufficiently to establish successional thresholds difficult to reverse without species augmentation. Juniper (Juniperus virginiana L.) is expanding in North American tallgrass prairie, but it is currently unknown if encroachment creates successional restrictions that limit restoration potential. We selected 16 50×50-m sites with juniper canopy cover ranging from zero to approximately 75% in tallgrass prairie near Stillwater, Oklahoma, USA. Juniper trees were removed from 7 of the sites along the gradient of juniper canopy cover. Canopy cover of plant species and herbaceous plant productivity were estimated at each site 1 year before and 1, 2, and 5 years after tree removal. Before trees were removed, plant species richness and productivity declined as juniper canopy cover increased, and plant community composition dissimilarity of reference sites increased as juniper canopy cover increased. These relationships remained consistent on all non-removal sites throughout the study. The first year after juniper removal, species richness increased on all removal sites compared to intact sites and productivity on removal sites increased two years after removal. Plant community dissimilarity between reference sites and juniper removal sites remained relatively high (30–60%) the first two years after tree removal on all removal sites, but dissimilarity was about 22% 5 years after juniper removal. Within 5 years, removal sites were comparable to reference plant communities. Grassland restoration frequently requires species manipulation and additional seeding, particularly when overcoming successional limitations. Juniper encroachment into tallgrass prairie alters plant community species composition and productivity. However, in our study, juniper associated succession limitations were not apparent, and complete autogenic restoration was achieved within 5 years without seeding or species manipulation.

Contrasting effects of natural and anthropogenic stressors on beta diversity in river organisms

AbstractAimWe hypothesized that mechanisms underlying beta diversity in rivers would differ between gradients where (1) natural stressors result in progressive species turnover with high specificity and (2) anthropogenic stressors result in the loss of specialist taxa thus giving rise to nestedness.LocationGreat Britain, the Iberian Peninsula and the Himalayan Mountains.MethodsWe analysed five datasets describing benthic macroinvertebrates sampled along natural (elevation, salinity) and anthropogenic (acidity, metals, land use) stress gradients. Predictions were tested by fitting models relating species richness and beta‐diversity components (total, turnover and nestedness dissimilarities) to putative stress intensity (i.e. the degree to which a particular environmental constraint filters species occurrence).ResultsStress intensity accounted for most of the variability in species richness (r2 = 0.64–0.93), which declined with increasing stress. Dissimilarity in community composition between locations increased with the difference in stress intensity for all datasets. For natural stressors, beta‐diversity patterns mainly reflected species turnover, whilst for anthropogenic stressors beta diversity mainly reflected nesting of subsets of species as stress intensity increased.Main conclusionsOur results support the hypothesis that natural and anthropogenic stressors generate contrasting patterns in beta diversity that arise through different mechanisms.

Soil preparation methods promoting ectomycorrhizal colonization and American chestnut Castanea dentata establishment in coal mine restoration

Summary The objective of this research was to evaluate soil subsurface methods that may aid in seedling establishment and encourage root colonization from a diverse group of ectomycorrhizal (ECM) fungi during restoration projects. American chestnut Castanea dentata Marsh. Borkh. and backcrossed chestnuts seedlings were planted on a reclaimed coal mine site in central Ohio, USA. Roots from chestnut seedlings planted in the plots that were cross‐ripped, plowed and disked, or a combination of treatments were sampled for ECM fungi and compared with control plots. The presence and identification of native ECM were determined by fungal DNA sequencing of the internal‐transcribed (ITS) region. After two growing seasons, mechanical soil treatments resulted in seedlings with significantly more ECM species when compared to seedlings grown in the control plots (P < 0·0001). A nonmetric multidimensional scaling ordination followed by a permutational manova confirmed significant dissimilarities in community composition between the control and mechanically treated plots (F = 0·24, P = 0·015). Ectomycorrhizal root colonization was significantly higher on the chestnut seedlings sampled from the mechanically treated plots when compared to the control plots (F = 10·63, P < 0·0001). Differences did not exist among the three mechanical treatments. There was also a significant increase in above‐ground seedling growth in the plots that were treated with a surface soil method (F = 15·72, P < 0·0001). It is not clear whether ECM activity was the driver of plant growth; regardless, both are strong indicators of healthy tree establishment. Synthesis and applications. This study illustrates that the use of soil subsurface methods increased ectomycorrhizal (ECM) activity and seedling growth. Employing methods that encourage the root colonization by beneficial ECM and promote healthy seedling establishment may aid the long‐term survival of chestnuts in restoration projects. This can be applied to other hardwood seedlings used in reforestation in soils compacted after anthropogenic disturbances.

Seagrass bed patchiness: effects on epifaunal communities in San Diego Bay, USA

Seagrass habitat structure influences epifaunal density, diversity, community composition and survival, but covariation of structural elements at multiple scales (e.g., shoot density or biomass per unit area, patch size, and patch configuration) can confound studies attempting to correlate habitat structure with ecological patterns and processes. In this study, we standardized simulated seagrass shoot density and bed area among artificial seagrass beds in San Diego Bay, California, USA to evaluate the singular effect of seagrass bed configuration (“patchiness”) on the density and diversity of seagrass epifauna. Artificial seagrass beds all were 1 m 2, but were composed of a single large patch (“continuous” treatment), four smaller patches (“patchy” treatment), or 16 very small patches (“very patchy” treatment). We allowed epifauna to colonize beds for 1 month, and then sampled beds monthly over the next 3 months. Effects of seagrass bed patchiness on total epifaunal density and species-specific densities were highly variable among sampling dates, and there was no general trend for the effects of fragmentation on epifaunal densities to be positive or negative. Epifaunal diversity (measured as Simpson's index of diversity) was highest in very patchy or patchy beds on two out of the three sampling dates. Very patchy beds exhibited the highest dissimilarity in community composition in the first two sampling periods (August and September), but patchy beds exhibited the highest dissimilarity in the third sampling period (October). Our results indicate that seagrass patch configuration affects patterns of epifaunal density, diversity, and community composition in the absence of covarying bed area or structural complexity, and that patchy seagrass beds may be no less valuable as a habitat than are continuous seagrass beds. The spatial pattern employed when harvesting or planting seagrass may influence epifaunal habitat use and should be a key consideration in restoration plans.

Using gradients in tidal restriction to evaluate nekton community responses to salt marsh restoration

Few studies concerning tide-restricted and restoring salt marshes emphasize fishes and decapod crustaceans (nekton) despite their ecological significance. This study quantifies nekton utilization of three New England salt marshes under tide-restricted and restoring conditions (Hatches Harbor, Massachusetts; Sachuest Point and Galilee, Rhode Island). The degree of tidal restriction differed among marshes allowing for an examination of nekton utilization patterns along a gradient of tidal restriction and subsequent restoration. Based on sampling in shallow subtidal creeks and pools, nekton density and richness were significantly lower in the restricted marsh compared to the unrestricted marsh only at the most tide-restricted site (Sachuest Point). The dissimilarity in community composition between the unrestricted and restricted marsh sites increased with more pronounced tidal restriction. The increase in nekton density resulting from tidal restoration was positively related to the increase in tidal range. Species richness only increased with restoration at the most tide-restricted site; no significant change was observed at the other two sites. These patterns suggest that only severe tidal restrictions significantly reduce the habitat value of New England salt marshes for shallow subtidal nekton. This study suggests that the greatest responses by nekton, and the most dramatic shift towards a more natural nekton assemblage, will occur with restoration of severely restricted salt marshes.