Dissimilarity In Community Composition Research Articles

P1328 Reduced salivary alpha-diversity in Inflammatory Bowel Disease: Systematic review and meta-analysis of 1000 IBD patients – a role for oral microbiome as a marker of downstream dysbiosis in IBD

Abstract Background The gut microbiome is involved in the pathogenesis of CD, but the extent to which the oral microbiome contributes to this—and how it can be utilised for disease monitoring and therapeutics—remains under-explored. We aimed to characterise compositional differences in the oral microbiome of patients with IBD by conducting a systematic review and meta-analysis of the literature. Methods Medline, Embase, Web of Science, Cochrane, and SCOPUS were searched for articles published from inception to 1st February 2024. Primary screening and extraction were performed in duplicate. The extracted dataset included: disease phenotype, sampling data, diversity metrics, relative abundance analysis and sequencing/metadata availability. Random effects meta-analysis of the standardised mean difference of Shannon diversity was performed for IBD sub-types and disease activity. Results The initial search identified 1367 after removing duplicates; 37 studies were selected for full-text review, with 22 meeting the inclusion criteria. (Figure 1) Alpha diversity was reported in 20/22 (91%) of studies. Comparing salivary Shannon diversity of 976 undifferentiated IBD patients with 566 controls shows a significant reduction in patients with IBD (standardised mean difference [95% CI]: -0.29 [-0.54, -0.05]). In patients with high disease activity, there was a significant reduction in salivary Shannon diversity (IBD n = 133, control n = 181) (standardised mean difference [95% CI]: -0.51 [-0.98, -0.04]), which is lost when low activity patients are examined (IBD n = 128, control n = 170) (standardised mean difference [95% CI]: -0.12 [-0.46, 0.22]). (Figure 2) When examining beta diversity, significant dissimilarity in community composition between patients with IBD and controls was reported in 15/20 (75%) of studies. Relative abundance data of oral sites at a genus level was reported in 11/22 (50%) of studies. Changes are most frequently reported in the dominant phyla of the oral cavity (Bacillota, Bacteroidota, Actinobacter, and Pseudomonadota). The most frequently increased genera in IBD patients were Prevotella (4/11, 36%), Veilonella (3/11, 27%), Atopobium (3/11, 27%), and Megasphaera (3/11, 27%). Conclusion Based on this systematic review, there is evidence of distinct alterations in the oral microbiome composition of patients with IBD compared to controls which underscores the role of the oral microbiome as a potential indicator of downstream dysbiosis and crucial early immune-crosstalk in the oral cavity.

Difference in Community Structure and Function of Bacteria Attached to Stems and Leaves of Potamogeton crispus Compared to that of Bacteria in the Overlying Water and Sediment

The stems and leaves of submerged macrophytes usually grow below the water surface and could provide a good biological carrier for the colonization and growth of planktonic bacteria in water. Therefore, attached bacteria on the stem and leaf surfaces of submerged macrophytes are important components and play a crucial role in aquatic ecosystems. To further understand the structure characteristics and functional differences of the bacterial community attached to the stems and leaves of submerged macrophytes, the submerged macrophytes Potamogeton crispus and the overlying water and sediment were sampled and analyzed in this study. The results showed that a total of 10 320 OTUs were detected in the P. crispus samples, the overlying water samples, and the sediment samples. These OTUs included 64 phyla, 189 classes, 448 orders, 721 families, and 1 366 genera. The richness and diversity of bacterial communities in sediments were the highest, followed by the stem and leaves of P. crispus, and the alpha diversity index of planktonic bacteria in water was the lowest. Significant differences （P<0.05） were observed among the four alpha diversity indices of the three source samples. Bacterial communities with greater similarity were obtained from the same source samples, but there was more distinct community composition dissimilarity in bacteria collected from the submerged macrophytes and the overlying water and sediment samples （P<0.05）. At the level of phylum, order, and genus classification, the relative abundance of most dominant bacterial species, non-dominant species, and occasional species showed significant differences among the three source samples （P<0.05）. Proteobacteria, Actinobacteria, and Bacteroidetes were common dominant bacterial phyla for the three source samples, while Firmicutes were unique dominant phyla for attachment bacteria on the plant stem and leaves of P. crispus. There were differences in carbohydrate metabolism, energy metabolism, amino acid metabolism, cofactors, and vitamin metabolism among the three source samples （P<0.05）. The relative abundance of chemical heterotrophic and oxidative heterotrophic functional types in the stem and leaf samples of P. crispus was higher than that in the overlying water and sediment samples. In addition, higher nitrate reduction, nitrogen respiration, and nitric acid respiration functions were observed in sediment samples. To summarize, the stems and leaves have the potential to encourage bacterial colonization and create a unique bacterial community on the surface of submerged macrophytes. Submerged P. crispus macrophytes and their surroundings （water and sediment） play different roles in the biogeochemical cycling of nutrients in the freshwater ecosystem.

Functional Diversity of Macroinvertebrate Communities in River Nature Reserves of Spain

In recent decades, aquatic ecosystems have suffered a series of impacts that have made them some of the most threatened ecosystems on a global scale. So, protection measures are needed to conserve the biodiversity we find in some of the less impacted ecosystems. In the Spanish legislation, a category arose for this purpose in lotic ecosystems, the River Natural Reserve (RNR). In this work, we analyse the taxonomic and functional diversity of 145 macroinvertebrate biocoenoses from 128 different RNRs belonging to 10 different basins and representing 18 typologies. Most of the analysed biocoenoses have an overall high taxonomic diversity, with some exceptions corresponding to particular reaches suffering occasional disturbances or with very special conditions. An intermediate functional homogeneity has been also detected, related to a relatively low average functional richness. We also found medium levels of functional evenness, a high functional divergence, and low functional dispersion and Rao index values, the latter supporting similarities among taxa in functional terms. In our studied systems, there is high taxa turnover, but functional turnover is very low. This means that most of the trait dissimilarity between taxa is found within a community, but not among communities, though there are relatively strong dissimilarities in community composition. Our results support the fact that the RNRs are protecting communities of great diversity, not only taxonomic, but also functional, which contributes to the proper functioning of the ecosystems found in these stream reaches. Thus, the analysis of the functional diversity of the communities, as in the present approach, should be implemented to identify and prioritize protection of reaches with higher functional diversity, where enhanced ecosystem functioning can be expected.

Zebrafish (Danio rerio) behavioral phenotypes not underscored by different gut microbiota.

Different animal behavioral phenotypes maintained and selectively bred over multiple generations may be underscored by dissimilar gut microbial community compositions or not have any significant dissimilarity in community composition. Operating within the microbiota-gut-brain axis framework, we anticipated differences in gut microbiome profiles between zebrafish (Danio rerio) selectively bred to display the bold and shy personality types. This would highlight gut microbe-mediated effects on host behavior. To this end, we amplified and sequenced a fragment of the 16S rRNA gene from the guts of bold and shy zebrafish individuals (n=10) via Miseq. We uncovered no significant difference in within-group microbial diversity nor between-group microbial community composition of the two behavioral phenotypes. Interestingly, though not statistically different, we determined that the gut microbial community of the bold phenotype was dominated by Burkholderiaceae, Micropepsaceae, and Propionibacteriaceae. In contrast, the shy phenotype was dominated by Beijerinckaceae, Pirelullacaeae, Rhizobiales_Incertis_Sedis, and Rubinishaeraceae. The absence of any significant difference in gut microbiota profiles between the two phenotypes would suggest that in this species, there might exist a stable "core" gut microbiome, regardless of behavioral phenotypes, and or possibly, a limited role for the gut microbiota in modulating this selected-for host behavior. This is the first study to characterize the gut microbial community of distinct innate behavioral phenotypes of the zebrafish (that are not considered dysbiotic states) and not rely on antibiotic or probiotic treatments to induce changes in behavior. Such studies are crucial to our understanding of the modulating impacts of the gut microbiome on normative animal behavior.

Climate conditions are primary predictors of the regional‐scale spatial diversity patterns of ectomycorrhizal fungi

AbstractAimSpatial models are valuable for revealing biodiversity patterns but are less commonly applied to soil microbes than to aboveground macroorganisms. Ectomycorrhizal (EM) fungi are symbiotic microbes with high taxonomic and functional diversity that are associated with forest trees. We aimed to predict regional‐scale spatial patterns of EM fungal richness and community composition.LocationForests and subalpine ecosystems in Japan, from Hokkaido to Okinawa.TaxonEM fungi (Asco‐ and Basidiomycetes).MethodsWe used EM fungal DNA sequence data from 1507 soil cores at 39 sites covering a wide range of environmental conditions. The random forest machine learning approach was applied to determine the relative importance of environmental variables (i.e. climate, soil and ecosystem productivity) and to make spatial predictions. The spatial patterns of EM fungal richness and community composition were mapped at 1‐km2 grid resolution.ResultsTemperature generally had a strong influence on EM fungal richness and community composition dissimilarity. Our regional spatial analysis revealed that (1) EM fungal richness was higher in northeastern and montane regions than in southwestern regions and low‐elevation plains, (2) different EM fungal lineages exhibited contrasting spatial diversity patterns and (3) community composition dissimilarity shifted sharply from high to low elevations, and gradually from northeastern to southwestern regions, mainly in relation to climate gradients. Areas with low applicability for spatial modelling were identified based on multidimensional environmental spaces, which will help to prioritize data collection for future research.Main ConclusionsOur study provides a baseline of the potential spatial patterns of EM fungal communities, which were explained primarily by climate variables and secondarily by soil factors and ecosystem productivity. The predicted spatial patterns may be valuable for identifying diversity hotspots and advancing the assessment of climate change impacts on ecologically important root‐associated fungi.

Multiple anthropogenic stressors influence the taxonomic and functional homogenization of macroinvertebrate communities on the mainstream of an urban-agricultural river in China

Biodiversity loss is caused by intensive human activities and threatens human well-being. However, less is known about how the combined effects of multiple stressors on the diversity of internal (alpha diversity) and multidimensional (beta diversity) communities. Here, we conducted a long-term experiment to quantify the contribution of environmental stressors (including water quality, land use, climate factors, and hydrological regimes) to macroinvertebrate communities alpha and beta diversity in the mainstream of the Songhua River, the third largest river in China, from 2012 to 2019. Our results demonstrated that the alpha and beta diversity indices showed a decline during the study period, with the dissimilarity in community composition between sites decreasing significantly, especially in the impacted river sections (upper and midstream). Despite overall improvement in water quality after management intervention, multiple human-caused stressors still have led to biotic homogenization of macroinvertebrate communities in terms of both taxonomic and functional diversities in the past decade. Our study revealed the increased human land use explained an important portion of the variation of diversities, further indirectly promoting biotic homogenization by changing the physical and chemical factors of water quality, ultimately altering assemblage ecological processes. Furthermore, the facets of diversity have distinct response mechanisms to stressors, providing complementary information from the perspective of taxonomy and function to better reflect the ecological changes of communities. Environmental filtering determined taxonomic beta diversity, and functional beta diversity was driven by the joint efforts of stressors and spatial processes. Finally, we proposed that traditional water quality monitoring alone cannot fully reveal the status of river ecological environment protection, and more importantly, we should explore the continuous changes in biodiversity over the long term. Meanwhile, our results also highlight timely control of nutrient input and unreasonable expansion of land use can better curb the ecological degradation of rivers and promote the healthy and sustainable development of floodplain ecosystems.

Regenerated woody plants influence soil microbial communities in a subtropical forest

Forests are critical for supporting multiple ecosystem services such as climate change mitigation. Microbial diversity in soil provides important functions to maintain and regenerate forest ecosystems, and yet a critical knowledge gap remains in identifying the linkage between attributes of regenerated woody plant (RWP) communities and the diversity patterns of soil microbial communities in subtropical plantations. Here, we investigated the changes in soil microbial communities and plant traits in a nine hectare Chinese fir (Cunninghamia lanceolata; CF) plantation to assess how non-planted RWP communities regulate soil bacterial and fungal diversity, and further explore the potential mechanisms that structure their interaction. Our study revealed that soil bacterial richness was positively associated with RWP richness, whereas soil fungal richness was negatively associated with RWP basal area. Meanwhile, RWP richness was positively correlated with ectomycorrhizal (ECM) fungal richness but negatively correlated with the richness of both pathogenic and saprotrophic fungi, suggesting that the RWP-fungal richness relationship was trophic guild-specific. Soil microbial community beta diversity (i.e., dissimilarity in community composition) was strongly coupled with both RWP beta diversity and the heterogeneity of RWP basal area. Our study highlights the importance of community-level RWP plant attributes for the regulation of microbial biodiversity in plantation systems, which should be considered in forest management programs in the future.

From river to ocean: Connectivity and heterogeneity of aquatic ecosystems depicted by planktonic microeukaryotes

Understanding how the diverse habitats incubated a high diverse biosphere is a core question for biodiversity conservation. Community assembly of organisms in connected but different habitats could provide insight into this issue. As an important group of plankton, microeukaryotes are widely distributed in aquatic habitats and are sensible to ecological conditions. However, how the distribution of planktonic microeukaryotes from river to ocean are shaped by habitat connectivity and heterogeneity remains unclear. In order to assess the connectivity and heterogeneity of aquatic habitats, environmental DNA sequencing was used to profile the planktonic microeukaryotic communities in typical habitats throughout the major rivers, estuaries, coastal waters, and ocean of China, covering a geographic distance of 3530 km. The hypothesized “freshwater species pool (FSP)” and “marine species pool (MSP)” of planktonic microeukaryotes were confirmed by their significant dissimilarities in community composition. The planktonic microeukaryotic communities completed turnover of FSP-pattern and MSP-pattern within salinity range of 5–15 in estuaries of the river-to-ocean continuum. In this scale covering fresh and salty waters, the community assembly of planktonic microeukaryotes was driven primarily by habitat filtering rather than salinity nor geographic distance. Four types of habitat, i.e., river, estuary, tidal zone, and ocean, were outlined by their planktonic microeukaryotic communities, which depicted the habitat heterogeneity in this continuum. As to the constructive species in these habitats, 98.1 % of them were shared between at least two types of habitat and 41.3 % of them shared among all habitats. These shared constructive species depicted the habitat connectivity of aquatic ecosystems from river to ocean. The findings suggest that the assessment of planktonic microorganism assemblages is a potential approach to indicate habitat diversity in connected aquatic ecosystems.

Organic and inorganic nutrients modulate taxonomic diversity and trophic strategies of small eukaryotes in oligotrophic oceans.

As the oligotrophic gyres expand due to global warming, exacerbating resource limitation impacts on primary producers, predicting changes to microbial assemblages and productivity requires knowledge of the community response to nutrient availability. This study examines how organic and inorganic nutrients influence the taxonomic and trophic composition (18S metabarcoding) of small eukaryotic plankton communities (< 200µm) within the euphotic zone of the oligotrophic Sargasso Sea. The study was conducted by means of field sampling of natural microbial communities and laboratory incubation of these communities under different nutrient regimes. Dissimilarity in community composition increased along a depth gradient, with a homogeneous protist community within the mixed layer and distinct microbial assemblages at different depths below the deep chlorophyll maximum. A nutrient enrichment assay revealed the potential of natural microbial communities to rapidly shift in composition in response to nutrient addition. Results highlighted the importance of inorganic phosphorus availability, largely understudied compared to nitrogen, in constraining microbial diversity. Dissolved organic matter addition led to a loss of diversity, benefiting a limited number of phagotrophic and mixotrophic taxa. Nutrient history of the community sets the physiological responsiveness of the eukaryotic community to changing nutrient regimes and needs to be considered in future studies.

Wintering waterbirds diversity and their impact factors in coastal lake wetlands of the Yangtze River in Jiangsu Province

长江及其中下游湖泊湿地组成了独特的江-河复合型生态系统，孕育了极高的生物多样性，是全球生物多样性研究的热点区域之一.该区域是东亚-澳大利西亚迁徙通道上最重要的水鸟越冬地之一，每年冬季有超过百万只水鸟在此越冬，因此，分析相关因素对越冬水鸟多样性的影响对维持其越冬安全具有重要意义.然而，目前相关研究多集中在如鄱阳湖、洞庭湖、升金湖等部分国家级保护区内，对经济较发达的江苏省沿江区域湖泊湿地水鸟多样性的研究仍不多见.本研究选择江苏长江沿江10处代表性湖泊湿地，于2018—2020年冬开展越冬水鸟调查，同时结合环境和人为因素，分析其对区域越冬水鸟多样性的影响.3次调查共记录到越冬水鸟42种109998只，隶属于6目9科.按地理区系划分，古北界16种，广布种15种，古北界-东洋界9种，东洋界2种；按生态类群划分，有游禽22种，涉禽20种.在10处湖泊湿地中，石臼湖水鸟物种数和数量均最多，金牛湖水鸟物种数和数量均为最低；Shannon-Wiener和Inverse-Simpson多样性指数最高的为石臼湖，最低分别为长荡湖和昆承湖.β多样性结果表明石臼湖水鸟群落与其它湿地相似性最低，长荡湖次之.β多样性分解分析结果显示，区域β多样性主要形成机制为物种替换.石臼湖对区域β多样性的相对贡献显著高于其它湖泊湿地，其次是长荡湖，相对贡献最低的是尚湖.线性模型结果表明：越冬水鸟丰富度与湿地总面积呈正相关，与缓冲区植被和水体面积呈负相关.人均GDP与越冬水鸟丰富度呈显著负相关.越冬水鸟物种数与湖泊湿地面积呈正相关，与人均GDP呈负相关.水鸟多样性指数受面积和人均GDP影响均不显著.江苏沿江地区是我国经济最发达的区域之一，对其越冬水鸟多样性及其影响因素开展研究进而提出相关保护建议，如持续开展越冬水鸟监测，及时发现保护空缺，提高对湿地周边区域土地利用状况的关注度等.本研究结果不仅为本地区越冬水鸟保护工作提供依据，同时也为上游经济相对薄弱但发展较快的地区开展相关保护工作提供参照.;The Yangtze River and its floodplain are unique for the extensive wetlands, recharged by summer monsoonal precipitation, laden with nutrients and sediment. It's the largest amount of shallow and seasonal flooded wetlands in the world, providing ecosystem services to tens of millions of people. The wetlands also support globally significant numbers of wintering waterbirds. Every year, more than 1 million waterbirds spend winter here. It is critical to understand the effects of different variables on wintering waterbirds diversity. So far, most of the research were focused on some National Nature Reserves, e.g. Lake Poyang, Lake Dongting and Lake Shengjin. The researches concerning wintering waterbirds diversity on lake wetlands located in the Lower Yangtze River floodplain in Jiangsu Province are still limited, where the economic is relatively developed. In this study, we systematically surveyed 10 representative wetlands along the Yangtze River in Jiangsu Province from 2018 to 2020 and then analyzed the effect of ecological and anthropogenic factors on waterbird abundance, species richness and diversities. In total, 109998 waterbird of 42 species were recorded, belonging to 6 orders and 9 families. Of them, 22 species are Natatores and the others are all Waders. In terms of the biogeographic distribution, 16 species belong to Paleartics, 15 species are wide distributive species, 9 species belong to Paleartics-Oriental, and 2 species belong to Oriental. Among the 10 lake wetlands, Lake Shijiu has the highest Shannon-Wiener and Inverse-Simpson diversity index, and the lowest are Lake Changdang and Lake Kuncheng respectively. In addition, the community composition dissimilarity (β diversity) between Lake Shijiu and the other lakes are the highest, following by Lake Changdang. Results of the decomposition of β diversity suggested that species replacement was the main process influencing regional β diversity. Lake Shijiu had a significant higher relative contribution to regional β diversity, followed by Lake Changdang, while Lake Shanghu had the lowest relative contribution. Wintering waterbird abundance positively correlated with total area of wetlands but negatively affected by vegetation area and water area in the buffer area, as well as the effect of per capita GDP. Number of wintering bird species positively correlated with total area of lake wetlands but negatively affected by per capita GDP. Area had no effects on both Shannon-Wiener and Inverse-Simpson indices. As one of the most developed areas in China, unveiling the effects of different variables on wintering waterbirds diversity may not only offer practical conservation measures for this area, for example, carrying out continuous waterbird monitoring projects, detecting conservation gaps and playing close attention on landscape changes of surrounding area, but also provide a good sample for the conservation work in up-stream areas of the Yangtze River where the economic is ongoing developing.

Profiling the microbial community structure and functional diversity of a dam‐regulated river undergoing gravel bar restoration

Abstract Comprehensive restoration programs are expected to influence sediment‐associated microbial community structure and functional diversity following changes attributed to the restoration of habitat characteristics in the dam‐impacted channel. To address if the construction or recreation of in‐channel structures, i.e., gravel bars, by implementing gravel augmentation and ecological flow restoration, resulted in habitat restoration and enhanced environmental heterogeneity, we profiled the community composition, estimated diversity, and annotated putative metabolic functions of the sediment microbial communities of the dam‐regulated Trinity River in northern California. Our results provided supporting evidence on the positive impact of habitat restoration conducted in the Trinity River with the non‐dam influenced, undisturbed tributaries as the basis of comparison. In addition, gravel bar recreation and restoration contributed to the increased microbial beta diversity, possibly through the increased environmental heterogeneity at the river scale. The significant positive correlation between the taxonomic and functional diversity of the identified microbial taxa suggests that differences in the detected putative metabolic functions were closely related to dissimilarities in community composition. We also provided valuable insights into the potential microbial processes in the sediment that might be contributing to the biogeochemical processes carried out by the microbial communities in the river. The results of this study have implications on the impact of construction and restoration of gravel bars in a dam‐impacted river on environmental heterogeneity and how this influences the taxonomic and functional diversities of sediment‐associated microbial communities.

Anuran assemblage changes along small-scale phytophysiognomies in natural Brazilian grasslands

ABSTRACT We studied the species composition of frogs in two phytophysiognomies within Pampa biome (grassland and forest) of a Ramsar site in southern Brazil to assess the distribution of species and dissimilarities in community composition on a small spatial scale. We tested the hypothesis that the vegetation structure and the types of land cover present in each physiognomy influence species distribution and the compositional dissimilarity patterns between locations. We sampled individuals using pitfall traps and active search in the areas around the traps. We evaluated the existence of these differences by using permutational multivariate analysis of variance and multivariate dispersion. We found that the compositional dissimilarity was higher between the sampling sites from different phytophysiognomies than within the same phytophysiognomy. Also, the difference in anuran species composition between the sampling sites within the forest was considerably high. These differences were mainly due to the type of land cover present in each sampled site. Based on our results, we could assume that the phytophysiognomies evaluated here offer quite different colonization opportunities for anurans, especially those related to microhabitat characteristics, such as microclimate variables. Still, the presence of different types of land cover seems to be a decisive factor for the maintenance of some anuran species, since these can serve as an important source for obtaining food resources, in addition to facilitating the dispersion of individuals within and between locals, serve as sites for the regulation of physiological functions and also refuges against predators.

High throughput shotgun sequencing of eRNA reveals taxonomic and derived functional shifts across a benthic productivity gradient.

Benthic macrofauna is regularly used in monitoring programmes, however the vast majority of benthic eukaryotic biodiversity lies mostly in microscopic organisms, such as meiofauna (invertebrates<1mm) and protists, that rapidly responds to environmental change. These communities have traditionally been hard to sample and handle in the laboratory, but DNA sequencing has made such work less time consuming. While DNA sequencing captures both alive and dead organisms, environmental RNA (eRNA) better targets living organisms or organisms of recent origin in the environment. Here, we assessed the biodiversity of three known bioindicator microeukaryote groups (nematodes, foraminifera, and ciliates) in sediment samples collected at seven coastal sites along an organic carbon (OC) gradient. We aimed to investigate if eRNA shotgun sequencing can be used to simultaneously detect differences in (i) biodiversity of multiple microeukaryotic communities; and (ii) functional feeding traits of nematodes. Results showed that biodiversity was lower for nematodes and foraminifera in high OC (6.2%-6.9%), when compared to low OC sediments (1.2%-2.8%). Dissimilarity in community composition increased for all three groups between Low OC and High OC, as well as the classified feeding type of nematode genera (with more nonselective deposit feeders in high OC sediment). High relative abundant genera included nematode Sabatieria and foraminifera Elphidium in high OC, and Cryptocaryon-like ciliates in low OC sediments. Considering that future sequencing technologies are likely to decrease in cost, the use of eRNA shotgun sequencing to assess biodiversity of benthic microeukaryotes could be a powerful tool in recurring monitoring programmes.

A Case Study of Nematode Communities’ Dynamics along Successional Paths in the Reclaimed Landfill

We assessed the abundance and composition of nematode communities in soil under herbaceous vegetation in reclaimed landfill sites at different ages after closure (3, 10 and 14 years) compared to those in neighboring semi-natural grazed grasslands (reference sites). We further applied network analysis based on the co-occurrence patterns of nematodes. Nematode abundance decreased between 3 and10 years of regeneration, but significantly increased from 10 to 14 years of regeneration. The number and identity of genera were comparable along the succession; however, there were dissimilarities in community composition during early- and mid-succession. The diversity, community composition and abundance at the sites after 14 years of regeneration converged with those at the reference sites. Moreover, changes during succession were not accompanied by the maturation of the soil food web, as demonstrated by Enrichment and Channel indices. In all the networks, centrality and modularity metrics differed significantly from those for random networks, whereas cohesion metrics showed no difference. All the networks exhibited Small-worldness indices higher than one, demonstrating that the networks of the interactions among genera at all the sites shared features that matched both random and non-random networks. The succession trajectory in reclaimed landfills was represented by a sequence of changes that differed in relation to the variable under consideration; network parameters tended to converge with those of a relatively resistant reference community, while the Enrichment and Channel indices did not. Additionally, the succession trajectory was not linear or steady; only the Channel index and Worldness index showed linear responses to succession time. However, across all the successional stages, the resource status remained basal or degraded while the nematode communities had an enhanced ability to cope with sudden changes.

Spatial variability of hosts, parasitoids and their interactions across a homogeneous landscape.

Species assemblages and their interactions vary through space, generating diversity patterns at different spatial scales. Here, we study the local‐scale spatial variation of a cavity‐nesting bee and wasp community (hosts), their nest associates (parasitoids), and the resulting antagonistic network over a continuous and homogeneous habitat. To obtain bee/wasp nests, we placed trap‐nests at 25 sites over a 32 km2 area. We obtained 1,541 nests (4,954 cells) belonging to 40 host species and containing 27 parasitoid species. The most abundant host species tended to have higher parasitism rate. Community composition dissimilarity was relatively high for both hosts and parasitoids, and the main component of this variability was species turnover, with a very minor contribution of ordered species loss (nestedness). That is, local species richness tended to be similar across the study area and community composition tended to differ between sites. Interestingly, the spatial matching between host and parasitoid composition was low. Host β‐diversity was weakly (positively) but significantly related to geographic distance. On the other hand, parasitoid and host‐parasitoid interaction β‐diversities were not significantly related to geographic distance. Interaction β‐diversity was even higher than host and parasitoid β‐diversity, and mostly due to species turnover. Interaction rewiring between plots and between local webs and the regional metaweb was very low. In sum, species composition was rather idiosyncratic to each site causing a relevant mismatch between hosts and parasitoid composition. However, pairs of host and parasitoid species tended to interact similarly wherever they co‐occurred. Our results additionally show that interaction β‐diversity is better explained by parasitoid than by host β‐diversity. We discuss the importance of identifying the sources of variation to understand the drivers of the observed heterogeneity.

Correction to 'Microbes and macro-invertebrates show parallel β-diversity but contrasting α-diversity patterns in a marine natural experiment'.

Documenting ecological patterns across spatially, temporally and taxonomically diverse ecological communities is necessary for a general understanding of the processes shaping biodiversity. A major gap in our understanding remains the comparison of diversity patterns across a broad spectrum of evolutionarily and functionally diverse organisms, particularly in the marine realm. Here, we aim to narrow this gap by comparing the diversity patterns of free-living microbes and macro-invertebrates across a natural experiment provided by the marine lakes of Palau: geographically discrete and environmentally heterogeneous bodies of seawater with comparable geological and climatic history, and a similar regional species pool. We find contrasting patterns of α-diversity but remarkably similar patterns of β-diversity between microbial and macro-invertebrate communities among lakes. Pairwise dissimilarities in community composition among lakes are positively correlated between microbes and macro-invertebrates, and influenced to a similar degree by marked gradients in oxygen concentration and salinity. Our findings indicate that a shared spatio-temporal and environmental context may result in parallel patterns of β-diversity in microbes and macro-invertebrates, in spite of key trait differences between these organisms. This raises the possibility that parallel processes also influence transitions among regional biota across the tree of life, at least in the marine realm.

Microbes and macro-invertebrates show parallel β-diversity but contrasting α-diversity patterns in a marine natural experiment.

Documenting ecological patterns across spatially, temporally and taxonomically diverse ecological communities is necessary for a general understanding of the processes shaping biodiversity. A major gap in our understanding remains the comparison of diversity patterns across a broad spectrum of evolutionarily and functionally diverse organisms, particularly in the marine realm. Here, we aim to narrow this gap by comparing the diversity patterns of free-living microbes and macro-invertebrates across a natural experiment provided by the marine lakes of Palau: geographically discrete and environmentally heterogeneous bodies of seawater with comparable geological and climatic history, and a similar regional species pool. We find contrasting patterns of α-diversity but remarkably similar patterns of β-diversity between microbial and macro-invertebrate communities among lakes. Pairwise dissimilarities in community composition among lakes are positively correlated between microbes and macro-invertebrates, and influenced to a similar degree by marked gradients in oxygen concentration and salinity. Our findings indicate that a shared spatio-temporal and environmental context may result in parallel patterns of β-diversity in microbes and macro-invertebrates, in spite of key trait differences between these organisms. This raises the possibility that parallel processes also influence transitions among regional biota across the tree of life, at least in the marine realm.

Comparison of community composition between Microcystis colony-attached and free-living bacteria, and among bacteria attached with Microcystis colonies of various sizes in culture

A better understanding of the distribution pattern of bacterial community in the Microcystis phycosphere will aid in elucidating the role of bacteria in the formation of cyanobacterial bloom. In the present study, we aimed to compare community composition between Microcystis colony-attached and free-living bacteria, as well as among bacteria attached with Microcystis colonies of various sizes in culture. In the exponentially growing cyanobacterial cultures, Proteobacteria was the most dominant phylum in each colony-attached bacterial community, whereas Bacteroidetes was the most dominant phylum in each free-living bacterial community. The analysis using an indirect PCA model and Bray–Curtis dissimilarity index indicated that the dissimilarity between colony-attached and free-living bacterial communities was greater in the exponentially growing cyanobacterial cultures, and it became smaller in the stationary cultures of Microcystis. In the exponential growth phase of Microcystis, the relative abundance of Proteobacteria in colony-attached bacterial communities tended to decrease with decreasing colony size, whereas the relative abundance of Bacteroidetes in colony-attached bacterial communities tended to increase. In the exponential growth phase of Microcystis, the community composition dissimilarity among bacteria attached with Microcystis colonies of various sizes could be ranked in a descending order as follows: > 100 µm versus 100 µm versus 50–100 µm. Our data indicated that the community composition of Microcystis colony-attached bacteria was different from that of free-living bacteria, and the colony size of Microcystis played an important role in structuring the community composition of Microcystis-attached bacteria.

Spatial and temporal analysis of beta diversity in the Barro Colorado Island forest dynamics plot, Panama

BackgroundEcologists are interested in assessing the spatial and temporal variation in ecological surveys repeated over time. This paper compares the 1985 and 2015 surveys of the Barro Colorado Forest Dynamics plot (BCI), Panama, divided into 1250 (20 m × 20 m) quadrats.Methods, spatial analysisTotal beta diversity was measured as the total variance of the Hellinger-transformed community data throughout the BCI plot. Total beta was partitioned into contributions of individual sites (LCBD indices), which were tested for significance and mapped.Results, spatial analysisLCBD indices indicated the sites with exceptional community composition. In 1985, they were mostly found in the swamp habitat. In the 2015 survey, none of the swamp quadrats had significant LCBDs. What happened to the tree community in the interval?Methods, temporal analysisThe dissimilarity in community composition in each quadrat was measured between time 1 (1985) and time 2 (2015). Temporal Beta Indices (TBI) were computed from abundance and presence-absence data and tested for significance. TBI indices can be decomposed into B = species (or abundances-per-species) losses and C = species (or abundances-per-species) gains. B-C plots were produced; they display visually the relative importance of the loss and gain components, through time, across the sites.Results, temporal analysisIn BCI, quadrats with significant TBI indices were found in the swamp area, which is shrinking in importance due to changes to the local climate. A published habitat classification divided the BCI forest plot into six habitat zones. Graphs of the B and C components were produced for each habitat group. Group 4 (the swamp) was dominated by species (and abundances-per-species) gains whereas the five other habitat groups were dominated by losses, some groups more than others.ConclusionsWe identified the species that had changed the most in abundances in the swamp between T1 and T2. This analysis supported the hypothesis that the swamp is drying out and is invaded by species from the surrounding area. Analysis of the B and C components of temporal beta diversity bring us to the heart of the mechanisms of community change through time: losses (B) and gains (C) of species, losses and gains of individuals of various species. TBI analysis is especially interesting in species-rich communities where we cannot examine the changes in every species individually.

Influences of Canopy Nitrogen and Water Addition on AM Fungal Biodiversity and Community Composition in a Mixed Deciduous Forest of China

Nitrogen (N) deposition and precipitation could profoundly influence the structure and function of forest ecosystems. However, conventional studies with understory additions of nitrogen and water largely ignored canopy-associated ecological processes and may have not accurately reflected the natural situations. Additionally, most studies only made sampling at one time point, overlooked temporal dynamics of ecosystem response to environmental changes. Here we carried out a field trial in a mixed deciduous forest of China with canopy addition of N and water for 4 years to investigate the effects of increased N deposition and precipitation on the diversity and community composition of arbuscular mycorrhizal (AM) fungi, the ubiquitous symbiotic fungi for the majority of terrestrial plants. We found that (1) in the 1st year, N addition, water addition and their interactions all exhibited significant influences on AM fungal community composition; (2) in the 2nd year, only water addition significantly reduced AM fungal alpha-diversity (richness and Shannon index); (3) in the next 2 years, both N addition and water addition showed no significant effect on AM fungal community composition or alpha-diversity, with an exception that water addition significantly changed AM fungal community composition in the 4th year; (4) the increment of N or water tended to decrease the abundance and richness of the dominant genus Glomus and favored other AM fungi. (5) soil pH was marginally positively related with AM fungal community composition dissimilarity, soil NH4+-N and N/P showed significant/marginal positive correlation with AM fungal alpha-diversity. We concluded that the effect of increased N deposition and precipitation on AM fungal community composition was time-dependent, mediated by soil factors, and possibly related to the sensitivity and resilience of forest ecosystem to environmental changes.