Exploring the environmental influences and community assembly processes of bacterioplankton in a subtropical coastal system: Insights from the Beibu Gulf in China.

Due to rapid urbanization, the Beibu Gulf, a semi-closed gulf in the northwestern South China Sea, faces escalating ecological and environmental threats. Understanding the assembly mechanisms and driving factors of bacterioplankton in the Beibu Gulf is crucial for preserving its ecological functions and services. In the present study, we investigated the spatiotemporal dynamics of bacterioplankton communities and their assembly mechanisms in the Beibu Gulf based on the high-throughput sequencing of the bacterial 16 S rRNA gene. Results showed significantly higher bacterioplankton diversity during the wet season compared to the dry season. Additionally, distinct seasonal variations in bacterioplankton composition were observed, characterized by an increase in Cyanobacteria and Thermoplasmatota and a decrease in Proteobacteria and Bacteroidota during the wet season. Null model analysis revealed that stochastic processes governed bacterioplankton community assembly in the Beibu Gulf, with drift and homogenizing dispersal dominating during the dry and wet seasons, respectively. Enhanced deterministic assembly of bacterioplankton was also observed during the wet season. Redundancy and random forest model analyses identified the physical properties (e.g., temperature) and nutrient content (e.g., nitrate) of water as primary environmental drivers influencing bacterioplankton dynamics. Moreover, variation partitioning and distance-decay of similarity revealed that environmental filtering played a significant role in shaping bacterioplankton variations in this rapidly developed coastal ecosystem. These findings advance our understanding of bacterioplankton assembly in coastal ecosystems and establish a theoretical basis for effective ecological health management amidst ongoing global changes.

Scale-Dependent Influences of Distance and Vegetation on the Composition of Aboveground and Belowground Tropical Fungal Communities.

Fungi provide essential ecosystem services and engage in a variety of symbiotic relationships with trees. In this study, we investigate the spatial relationship of trees and fungi at a community level. We characterized the spatial dynamics for above- and belowground fungi using a series of forest monitoring plots, at nested spatial scales, located in the tropical South Pacific, in Vanuatu. Fungal communities from different habitats were sampled using metagenomic analysis of the nuclear ribosomal ITS1 region. Fungal communities exhibited strong distance-decay of similarity across our entire sampling range (3-110,000 m) and also at small spatial scales (< 50 m). Unexpectedly, this pattern was inverted at an intermediate scale (3.7-26 km). At large scales (80-110 km), belowground and aboveground fungal communities responded inversely to increasing geographic distance. Aboveground fungal community turnover (beta diversity) was best explained, at all scales, by geographic distance. In contrast, belowground fungal community turnover was best explained by geographic distance at small scales and tree community composition at large scales. Fungal communities from various habitats respond differently to the influences of habitat and geographic distance. At large geographic distances (80-110 km), community turnover for aboveground fungi is better explained by spatial distance, whereas community turnover for belowground fungi is better explained by plant community turnover. Future syntheses of spatial dynamics among fungal communities must explicitly consider geographic scale to appropriately contextualize community turnover.

Do the pattern and strength of species associations in ectoparasite communities conform to biogeographic rules?

We tested whether biogeographic patterns characteristic of species diversity and composition may also apply to community assembly by investigating geographic variation in the pattern (PSA) (aggregation versus segregation) and strength of species associations (SSA) in flea and mite communities harbored by small mammalian hosts in Western Siberia. We asked whether (a) there is a relationship between latitude and PSA or SSA and (b) similarities in PSA or SSA follow a distance decay pattern or if they are better explained by variation in environmental factors (altitude, amount of vegetation, precipitation, and air temperature). We used a sign of a co-occurrence metric (the C-score) as an indicator of PSA and its absolute standardized value as a measure of SSA. We analyzed data using logistic and linear models, generalized dissimilarity modeling (GDM), and a logistic version of the multiple regression on distance matrices (MRM). The majority of the C-scores of the observed presence/absence matrices indicated a tendency to species aggregation rather than segregation. No effect of latitude on PSA or SSA was found. The dissimilarity in PSA was affected by environmental dissimilarity in mite compound communities only. A relatively large proportion of the deviance of spatial variation in SSA was explained by the GDMs in infracommunities, but not component communities, and in only three (of seven) and two (of eight) host species of fleas and mites, respectively. The best predictors of dissimilarity in SSA in fleas differed between host species, whereas the same factor (precipitation) was the best predictor of dissimilarity in SSA in mites. We conclude that PSA and SSA in parasite communities rarely conform to biogeographic rules. However, when a biogeographic pattern is detected, its manifestation differs among hosts and between ectoparasite taxa.

Spatial structuring of soil microbial communities in commercial apple orchards.

Characterising spatial microbial community structure is important to understand and explain the consequences of continuous plantation of one crop species on the performance of subsequent crops, especially where this leads to reduced growth vigour and crop yield. We investigated the spatial structure, specifically distance-decay of similarity, of soil bacterial and fungal communities in two long-established orchards with contrasting agronomic characteristics. A spatially explicit sampling strategy was used to collect soil from under recently grubbed rows of apple trees and under the grassed aisles. Amplicon-based metabarcoding technology was used to characterise the soil microbial communities. The results suggested that (1) most of the differences in soil microbial community structure were due to large-scale differences (i.e. between orchards), (2) within-orchard, small-scale (1-5 m) spatial variability was also present, but spatial relationships in microbial community structure differed between orchards and were not predictable, and (3) vegetation type (i.e. trees or grass and their associated management) can significantly alter the structure of soil microbial communities, affecting a large proportion of microbial groups. The discontinuous nature of soil microbial community structure in the tree stations and neighbouring grass aisles within an orchard illustrate the importance of vegetation type and allied weed and nutrient management on soil microbial community structure.

Do abundance distributions and species aggregation correctly predict macroecological biodiversity patterns in tropical forests?

AIM: It has been recently suggested that different 'unified theories of biodiversity and biogeography' can be characterized by three common 'minimal sufficient rules': (1) species abundance distributions follow a hollow curve, (2) species show intraspecific aggregation, and (3) species are independently placed with respect to other species. Here, we translate these qualitative rules into a quantitative framework and assess if these minimal rules are indeed sufficient to predict multiple macroecological biodiversity patterns simultaneously. LOCATION: Tropical forest plots in Barro Colorado Island (BCI), Panama, and in Sinharaja, Sri Lanka. METHODS: We assess the predictive power of the three rules using dynamic and spatial simulation models in combination with census data from the two forest plots. We use two different versions of the model: (1) a neutral model and (2) an extended model that allowed for species differences in dispersal distances. In a first step we derive model parameterizations that correctly represent the three minimal rules (i.e. the model quantitatively matches the observed species abundance distribution and the distribution of intraspecific aggregation). In a second step we applied the parameterized models to predict four additional spatial biodiversity patterns. RESULTS: Species-specific dispersal was needed to quantitatively fulfil the three minimal rules. The model with species-specific dispersal correctly predicted the species-area relationship, but failed to predict the distance decay, the relationship between species abundances and aggregations, and the distribution of a spatial co-occurrence index of all abundant species pairs. These results were consistent over the two forest plots. MAIN CONCLUSIONS: The three 'minimal sufficient' rules only provide an incomplete approximation of the stochastic spatial geometry of biodiversity in tropical forests. The assumption of independent interspecific placements is most likely violated in many forests due to shared or distinct habitat preferences. Furthermore, our results highlight missing knowledge about the relationship between species abundances and their aggregation.

Biogeography of larval trematodes in the freshwater snail, Semisulcospira libertina: a comparison of the morphological and molecular approaches.

While biogeographic patterns of free-living organisms are well documented, the biogeography of parasitic fauna remains largely unclear. Due to morphological similarities, parasites are often difficult to identify without the aid of molecular genetics, further complicating the interpretation of their biogeographic patterns. We investigated trematode parasites infecting the East Asian freshwater snail Semisulcospira libertina to understand their biogeography and to evaluate how molecular approaches influence the interpretation of biogeographic patterns of the trematode fauna. We identified 46 genetically delimited species from 19 morphologically distinguishable trematodes infecting S. libertina and found that their species richness was negatively correlated to latitude. We also found that potential definitive host (fishes) richness and host body size were positively correlated with trematode species richness, suggesting that host attributes are essential factors shaping the biogeographic pattern in trematodes. These trends were observed irrespective of species identification methods, demonstrating that classical morphological identification can also effectively identify the latitudinal gradient pattern in trematodes. We further detected the distance decay of similarity in trematode communities, although this trend was only detectable in the biogeographic dataset based on molecular identification. Our study showed that morphological identification sufficiently reflects the latitudinal richness gradient while molecular identification is essential to estimate accurate local species richness and increase the resolution of the large-scale pattern of population similarities in the trematode communities.

Ecology of testate amoebae in waterbodies of the Central Highlands and South-Central Coast provinces of Vietnam with the description of new species Difflugia quangtrani sp. nov.

This study provides new data on ecology of testate amoebae in the waterbodies of the Central Highlands and South-Central Coast regions of Vietnam. A total of 108 species and subspecies including six new records for Vietnam were identified. One new species Difflugia quangtrani sp. nov. was described. Difflugia, Arcella, and Centropyxis were the most species-rich genera, and Centropyxis aculeata was the most common species. The results of NMDS and ANOSIM analyses for the first time showed significant differences in composition of tropical freshwater testate amoeba communities within both various types of waterbodies (reservoir, river, and wetland) and biotopes (plankton and benthos). Average species richness per sample in different types of waterbodies was similar, while that of plankton was statistically higher than in benthos. The distance decay of similarity in tropical freshwater testate amoeba community of both plankton and benthos was observed for the first time indicating the importance of geographical distance in testacean species composition changes between samples. Redundancy analyses followed by the forward selection have determined elevation, pH, and dissolved oxygen as significant factors that affect tropical freshwater testacean community. More large-scale climatic and small-scale hydrological and hydrochemical variables should be included into further studies to find out most important factors determining structure of freshwater testacean assemblages.

Effects of spatial distance and woody plant cover on beta diversity point to dispersal limitation as a driver of community assembly during postfire succession in a Mediterranean shrubland.

Beta diversity, and its components of turnover and nestedness, reflects the processes governing community assembly, such as dispersal limitation or biotic interactions, but it is unclear how they operate at the local scale and how their role changes along postfire succession. Here, we analyzed the patterns of beta diversity and its components in a herbaceous plant community after fire, and in relation to dispersal ability, in Central Spain. We calculated multiple-site beta diversity (ßSOR) and its components of turnover (ßSIM) and nestedness (ßSNE) of all herbaceous plants, or grouped by dispersal syndrome (autochory, anemochory, and zoochory), during the first 3 years after wildfire. We evaluated the relationship between pairwise beta diversity (ßsor), and its components (ßsim, ßsne), and spatial distance or differences in woody plant cover, a proxy of biotic interactions. We found high multiple-site beta diversity dominated by the turnover component. Community dissimilarity increased with spatial distance, driven mostly by the turnover component. Species with less dispersal ability (i.e., autochory) showed a stronger spatial pattern of dissimilarity. Biotic interactions with woody plants contributed less to community dissimilarity, which tended to occur through the nestedness component. These results suggest that dispersal limitation prevails over biotic interactions with woody plants as a driver of local community assembly, even for species with high dispersal ability. These results contribute to our understanding of postfire community assembly and vegetation dynamics.

Contrasting the assembly of phytoplankton and zooplankton communities in a polluted semi-closed sea: Effects of marine compartments and environmental selection.

Understanding the underlying mechanisms of community assembly is a major challenge in microbial ecology, particularly in communities composed of diverse organisms with different ecological characteristics. However, very little is known about the effects of marine compartments in shaping marine planktonic communities; primarily, how they are related to organism types and environmental variables. In this study, we used multiple statistical methods to explore the mechanisms driving phytoplankton and zooplankton metacommunity dynamics at the regional scale in the Bohai Sea, China. Clear geographic patterns were observed in both phytoplankton and zooplankton communities. Zooplankton showed a stronger distance-decay of similarity than phytoplankton, which had greater community differences between locations with further distances. Our analyses indicated that the zooplankton communities were primarily governed by species sorting versus dispersal limitation than the phytoplankton communities. Furthermore, we detected that zooplankton exhibited wider habitat niche breadths and dispersal abilities than phytoplankton. Our findings also showed that environmental pollution affected high trophic organisms via food webs; the presence of heavy metals in the Bohai Sea altered the abundance of some phytoplankton, and thus modified the zooplankton that feed on them.

Diversity patterns of free-living nematode assemblages in seagrass beds from the Cuban archipelago (Caribbean Sea).

Diversity patterns of free-living marine nematodes in tropical seagrass beds are understudied. Here, we describe the species richness and assemblage composition of nematodes in 13 seagrass sites covering the whole Cuban archipelago. Nematodes were collected from Thalassia testudinum seagrass beds and identified to species level. We provide a checklist of nematode species from seagrass beds. The species richness of nematode assemblages is high, with 215 species, 138 genus, 35 families, seven orders and two classes. That γ-diversity is higher than other studies and points to seagrass beds as diversity hotspots of free-living marine nematodes. Local species richness in seagrass bed sites is about 57 ± 17 species and broadly similar across the sites, despite the environmental heterogeneity. The geographical distance plays a weak, but significant, role on the decay of similarity likely affected by limited dispersal of nematodes. The pairwise similarity values, related to poor-coloniser nematodes, were twice more affected by the distance than those related to good-colonisers, possibly due to differential success of transport and settlement.

Biogeography of parasite abundance: latitudinal gradient and distance decay of similarity in the abundance of fleas and mites, parasitic on small mammals in the Palearctic, at three spatial scales.

We tested whether biogeographic patterns characteristic for biological communities can also apply to populations and investigated geographic patterns of variation in abundance of ectoparasites (fleas and mites) collected from bodies of their small mammalian hosts (rodents and shrews) in the Palearctic at continental, regional and local scales. We asked whether (i) there is a relationship between latitude and abundance and (ii) similarity in abundance follows a distance decay pattern or it is better explained by variation in extrinsic biotic and abiotic factors. We analysed the effect of latitude on mean intraspecific abundance using general linear models including proportional abundance of its principal host as an additional predictor variable. Then, we examined the relative effect of geographic distance, biotic and abiotic dissimilarities among regions, subregions or localities on the intraspecific dissimilarity in abundance among regions, subregions or localities using Generalized Dissimilarity Modelling. We found no relationship between latitude and intraspecific flea or mite abundance. In both taxa, environmental dissimilarity explained the largest part of the deviance of spatial variation in abundance, whereas the effect of the dissimilarity in the principal host abundance was of secondary importance and the effect of geographic distance was minor. These patterns were generally consistent across the three spatial scales, although environmental variation and dissimilarity in principal host abundance were equally important at the local scale in fleas but not in mites. We conclude that biogeographic patterns related to latitude and geographic distance do not apply to spatial variation of ectoparasite abundance. Instead, the geographic distribution of abundance in arthropod ectoparasites depends on their responses, mainly to the off-host environment and to a lesser extent the abundance of their principal hosts.

Which Latitudinal Gradients for Genetic Diversity?

A recent global analysis of GenBank DNA sequences from amphibians and mammals indicated consistent poleward decrease of intraspecific genetic diversity in both classes. We highlight that this result was biased by not accounting for distance decay of similarity and reanalyse the datasets, revealing distinct latitudinal gradients in mammals and amphibians.

Identifying the key taxonomic categories that characterize microbial community diversity using full-scale classification: a case study of microbial communities in the sediments of Hangzhou Bay.

Coastal areas are land-sea transitional zones with complex natural and anthropogenic disturbances. Microorganisms in coastal sediments adapt to such disturbances both individually and as a community. The microbial community structure changes spatially and temporally under environmental stress. In this study, we investigated the microbial community structure in the sediments of Hangzhou Bay, a seriously polluted bay in China. In order to identify the roles and contribution of all microbial taxa, we set thresholds as 0.1% for rare taxa and 1% for abundant taxa, and classified all operational taxonomic units into six exclusive categories based on their abundance. The results showed that the key taxa in differentiating the communities are abundant taxa (AT), conditionally abundant taxa (CAT), and conditionally rare or abundant taxa (CRAT). A large population in conditionally rare taxa (CRT) made this category collectively significant in differentiating the communities. Both bacteria and archaea demonstrated a distance decay pattern of community similarity in the bay, and this pattern was strengthened by rare taxa, CRT and CRAT, but weakened by AT and CAT. This implied that the low abundance taxa were more deterministically distributed, while the high abundance taxa were more ubiquitously distributed.