Community Similarity Research Articles

Soil Fungal Function Centralization Enhances the Decomposition of Fine Roots at Canopy Gap Borders

Canopy gaps can result in abiotic heterogeneities and diverse niches from gap borders to centers, potentially affecting fine root decompositions mediated by soil fungal communities. Despite extensive discussions on the relationship between soil fungi and fine root decomposition, the mechanism by which gap locations regulate fine root decomposition through the soil fungal community remains elusive. Here, we conducted an in situ field decomposition experiment of Chinese Toon (Toona senensis) fine roots in a low-efficiency weeping cypress (Cupressus funebris) plantation forest across three microhabitats: gap centers, gap borders, and closed canopy areas. Soil fungal communities were determined using internal transcribed spacer (ITS) sequencing after two years of field incubation. Results showed that soil properties and nutrient content in residual roots varied across the three microhabitats, with the gap borders exhibiting the highest decomposition rates. While fungal α-diversity remained relatively consistent, taxonomic compositions differed significantly. Decomposition rates did not show significant correlations with soil properties, observed fungal ASVs, or overall community composition. However, they positively correlated with the relative abundance of saprotrophic Sordariomycetes, which in turn positively correlated with soil total nitrogen (with a highest correlation), peaking at the gap borders. Overall community variations were primarily driven by soil temperature and magnesium content in residual roots. Further analysis revealed high fungal community similarities and low dispersal limitations between the gap borders and closed canopy areas, with more phylogenetically clustered communities at the borders. These results demonstrate that the gap borders possess a high decomposition rate, likely due to the centralization of functions driven by soil fungi such as saprotrophs existing in the “microbial seed bank” or migrating from closed canopy areas. These findings highlight the key role of soil fungi, especially saprotrophic fungi, in fine root decomposition at the gap borders, stressing the importance of soil fungi-driven mechanisms in nutrient cycling, and also informing sustainable forest management practices.

Heterogenization of microplastic communities in lakes of the Qinghai-Tibetan Plateau driven by tourism and transport activities

The Qinghai-Tibetan Plateau has a booming tourism industry and an increasingly sophisticated road system. There is a paucity of studies quantifying the contributions of anthropogenic and natural factors to microplastic pollution in remote plateau areas. In this study, water and sediment samples were collected from eight lake tourist attractions and four remote lakes in northern and southern regions of the Qinghai-Tibetan Plateau. Microplastics were detected in all samples, with a mean abundance of 0.78 items/L in water and 44.98 items/kg in sediment. The abundance of microplastics in the study area was lower than previously observed in more populated areas of China. Small-sized (<1 mm and 1–2 mm), fiber, and transparent microplastics were predominant, with polyethylene and polypropylene microplastics as the primary polymer types. The compositions of microplastic communities indicated that tourism and road networks were the major sources of microplastics in the lakes. Distance-decay models revealed greater influence of environmental distances on microplastic community similarity than geographic distance. Compared to climate factors, urban spatial impact intensity and traffic flow impact played a leading role in the structuring of microplastic communities in lake water and sediment. Our findings provide novel quantitative insights into the role of various factors in shaping the distribution patterns of microplastic communities in plateau lakes.

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.

Litter decomposition in pure and mixed plantations on the Loess Plateau, China: Lack of home-field advantage

Litter decomposition plays a critical role in the nutrient cycling of terrestrial ecosystems. According to the home-field advantage (HFA) hypothesis, litter decomposes more rapidly in its home habitat (where it originates) compared to other habitats (referred to as away). Although this hypothesis has been widely tested in natural forests, it remains controversial and lacks support for plantations, especially in dry ecosystems where microbial activities are limited. To clarify it, the present study investigated litter mass loss, nutrient dynamics, and decomposer communities in a 549-day reciprocal transplant experiment of litter decomposition in Robinia pseudoacacia (RP) and Hippophae rhamnoides (HR) pure plantations and their mixed plantations (5:5 and 8:2 ratios) on the Loess Plateau, China. The rate of mass, carbon (C), nitrogen (N) and phosphorus (P) loss in litter differed depending on litter type of species component and plantation type they were placed in. HR litter lost mass and released C, N, and P fastest, irrespective of plantation type. The overall mass loss of the four litter types were the fastest under 5:5 mixed plantations. However, litter did not decompose more rapidly in its home soil compared to the away soil. The structural equation modeling revealed that initial litter quality played a significant role in regulating the loss of C and N across decomposition stages, while the climate variations and microbial chemistry also contributed to the process. The similarity in soil microbial communities across plantation types, along with the limited interaction between litter and microbes in arid environments, could help elucidate the lack of HFA, with other factors such as the litter type exerting a minor influence. In summary, this study does not substantiate the hypothesis of home-field advantage but supports its context-dependency. Thus, regional heterogeneity should be taken into account when predicting the carbon cycle of forest ecosystems in future studies.

Archaea, bacteria and protists share a depth–decay relationship of community similarity in deep oceans

Abstract Identifying the general patterns of biogeography is vital for a better understanding of biological communities over space. However, there is a lack of well-understood biogeographic patterns of microbial communities in pelagic ecosystems. In this study, we simultaneously investigated archaeal, bacterial and protist communities using metabarcoding in the deep Pacific Ocean. Our results showed that archaea, bacteria and protists shared a depth–decay relationship of community similarity, indicating a decrease in community similarity with increasing differences in water depth. Environmental factors were more important than water depth in shaping this relationship, indicating that the sinking process, compared to environmental conditions, might be relatively minor in driving community variations across water columns. Our study suggests that the depth–decay relationship should be primarily examined in field investigations to better interpret the vertical dynamics of marine microbial communities, and more efforts are required to determine the mechanism underlying this important relationship.

Continental scale comparison of mycobiomes in Parmelia and Peltigera lichens from Turkey and South Korea

BackgroundLichens, traditionally considered as a simple partnership primarily between mycobiont and photobiont, are, in reality, complex holobionts comprised of a multitude of microorganisms. Lichen mycobiome represents fungal community residing within lichen thalli. While it is acknowledged that factors like the host lichen species and environmental conditions influence the structure of the lichen mycobiome, the existing research remains insufficient. To investigate which factor, host genus or location, has a greater impact on the lichen mycobiome, we conducted a comparative analysis of mycobiomes within Parmelia and Peltigera collected from both Turkey and South Korea, using high-throughput sequencing based on internal transcribed spacer region amplification.ResultsOverall, the lichen mycobiome was dominated by Capnodiales (Dothideomycetes), regardless of host or location. At the order level, the taxonomic composition was not significantly different according to lichen genus host or geographical distance. Hierarchical clustering of the top 100 abundant ASVs did not clearly indicate whether the lichen mycobiome was more influenced by host genus or location. Analyses of community similarity and partitioning variables revealed that the structure of the lichen mycobiome is more significantly influenced by location than by host genus. When analyzing the core mycobiome by host genus, the Peltigera mycobiome contained more ASV members than the Parmelia mycobiome. These two core mycobiomes also share common fungal strains, including basidiomycete yeast. Additionally, we used chi-squared tests to identify host genus-specialists and location-specialists.ConclusionsBy comparing lichen mycobiomes of the same genera across different countries, our study advances our comprehension of these microbial communities. Our study elucidates that, although host species play a contributory role, geographic distance exerts a more pronounced impact on the structure of lichen mycobiome. We have made foundational contributions to understanding the lichen mycobiome occupying ecologically crucial niches. We anticipate that broader global-scale investigations into the fungal community structures will provide more detailed insights into fungal residents within lichens.

Impact of environmental factors on small mammals and their fleas

Abstract Small mammals in the Horšianska dolina-Valley were researched first in 1984–86 and later in 2016–19. This paper seeks to identify and assess the species composition and dynamics of fleas (Siphonaptera) found in the valley on small mammals of Rodentia and Eulipotyphla and to compare findings from these two periods separated by thirty years. The results indicated deviations in small mammal and flea community similarity as well as in the small mammal indicator species for each habitat and flea indicator species for the small mammal species. A total 12 different species of small mammals were captured, and 12 flea species were collected. Eight flea species were detected in 1984–86 and ten species were found in 2016–19. In both periods A. penicilliger, C. assimilis, C. solutus, D. dasycnema, N. fasciatus were captured. The differences were that in the earlier period, the species uncovered were C. congener, P. bidentata, and P. soricis, while in the later period they were C. agyrtes, C. bisoctodentatus, M. turbidus, and R. integella. In the relationship between fleas and small mammals, C. solutus was the specific species for Apodemus flavicollis, while A. penicilliger and C. agyrtes were for Clethrionomys glareolus, and C. assimilis was for Microtus arvalis.

Species–environment sorting explains latitudinal patterns in spatiotemporal β‐diversity for freshwater macroinvertebrates

Understanding how and why β‐diversity varies along latitude is a long‐standing challenge in community ecology and rarely addressed in both space and time. We aimed to explore the spatiotemporal variations in macroinvertebrate β‐diversity and their underlying drivers in eight biogeographic regions covering a substantial latitudinal gradient of more than 40 degrees. By combining β‐diversity partitioning and distance decay of community similarity analyses, we found that subtropical β‐diversity varies more in space relative to variation in time compared with temperate β‐diversity, as we predicted. This is probably because subtropical β‐diversity is shaped by species–environment sorting (SS), caused by habitat heterogeneity and species specialization, more strongly in space relative to time than temperate β‐diversity. Our study highlights the importance of SS in shaping latitudinal gradients of β‐diversity in space and time.

Bacterial abundant taxa exhibit stronger environmental adaption than rare taxa in the Arctic Ocean sediments

Marine bacteria influence Earth’s environmental dynamics in fundamental ways by controlling the biogeochemistry and productivity of the oceans. However, little is known about the survival strategies of their abundant and rare taxa, especially in polar marine environments. Here, bacterial environmental adaptation, community assembly processes, and co-occurrence patterns between abundant and rare taxa were compared in the Arctic Ocean sediments. Results indicated that the diversity of rare taxa is significantly higher than that of abundant taxa, whereas the distance-decay rate of rare taxa community similarity is over 1.5 times higher than that of abundant taxa. Furthermore, abundant taxa exhibited broader environmental breadth and stronger phylogenetic signals compared to rare taxa. Additionally, the community assembly processes of the abundant taxa were predominantly governed by 81% dispersal limitation, while rare taxa were primarily influenced by 48% heterogeneous selection. The co-occurrence network further revealed the abundant taxa formed a more complex network to enhance their environmental adaptability. This study revealed the differences in environmental responses and community assembly processes between bacterial abundant and rare taxa in polar ocean sediments, providing some valuable insights for understanding their environmental adaptation strategies in marine ecosystems.

On the emergence of ecosystem decay: A critical assessment of patch area effects across spatial scales

Recent analyses suggest that positive patch area effects on biodiversity occur ubiquitously when comparing equal-effort samples from remnant habitat patches. The mechanisms underlying the emergence of this so-called “ecosystem decay” remain poorly understood despite conservation relevance. We leverage spatially-explicit information on the occurrence of plant species across the Swiss Alps (415 plots, 668 species) to test two mechanisms compatible with the emergence of patch-scale ecosystem decay: (i) plots sampled within small patches might have lower biodiversity than plots sampled within large patches (plot-scale decay hypothesis), and (ii) plots sampled within large patches might share a lower proportion of species (turnover hypothesis). We found that patch-scale ecosystem decay occurs also in our system. While plots sampled in large patches tended to be more dissimilar, supporting the turnover hypothesis, we did not find support for the plot-scale decay hypothesis. Additionally, distance between plots and elevational changes explain turnover between plots better than patch area effects. Taken together, these results indicate that applications of ecosystem decay in biodiversity conservation require a better understanding of the mechanisms that potentially underlie this pattern. Patch area effects might be less important than previously assumed when assessing landscape-scale biodiversity, because such effects can be confused with the effects of distance-decay in community similarity, environmental heterogeneity, and sampling effort. More broadly, our findings align with mounting evidence that protecting as much habitat as possible – regardless of whether such habitat exists continuous or fragmented – might be the most effective means to sustain biodiversity across human-dominated landscapes.

Environmental DNA metabarcoding reveals the effect of river slope on diadromous fish communities in island rivers

Understanding the natural factors that influence diadromous fish communities in river ecosystems is crucial for effective biodiversity management. However, this remains an unexplored and challenging task. Here, the relationship between river morphology and diadromous fish communities within rivers was explored. We focused on river slope and estuary size, as these may constrain their upstream migration and affect the availability of important nursery grounds for some species. Using environmental DNA metabarcoding, we investigated the diadromous fish communities within 12 rivers of subtropical Yakushima Island, southern Japan, and compared the community differences among rivers with different river slopes and estuary sizes. Fewer diadromous fish species were detected in rivers with steeper slopes and smaller estuaries. Additionally, the community similarity was greater among rivers with analogous gradients and estuary sizes. These results indicate that river slopes exert a species-selective effect on diadromous fish communities by affecting their upstream migration and estuarine habitat availability, thereby playing a crucial role in shaping the composition of these communities within rivers. Conserving gentle-gradient rivers with large estuaries would be crucial for preserving the diversity of diadromous fish species, which play a crucial role in shaping biodiversity especially in rivers of subtropical and tropical oceanic islands.

Seasonal dietary changes relate to gut microbiota composition depending on the host species but do not correlate with gut microbiota diversity in arthropod-eating lizards.

The animal gut microbiota is strongly influenced by environmental factors that shape their temporal dynamics. Although diet is recognized as a major driver of gut microbiota variation, dietary patterns have seldom been linked to gut microbiota dynamics in wild animals. Here, we analysed the gut microbiota variation between dry and rainy seasons across four Sceloporus species (S. aeneus, S. bicanthalis, S. grammicus and S. spinosus) from central Mexico in light of temporal changes in diet composition. The lizard microbiota was dominated by Firmicutes (now Bacillota) and Bacteroidota, and the closely related species S. aeneus and S. bicanthalis shared a great number of core bacterial taxa. We report species-specific seasonal changes in gut microbiota diversity and composition: greater alpha diversity during the dry compared to the rainy season in S. bicanthalis, the opposite pattern in S. aeneus, and no seasonal differences in S. grammicus and S. spinosus. Our findings indicated a positive association between gut bacterial composition and dietary composition for S. bicanthalis and S. grammicus, but bacterial diversity did not increase linearly with dietary richness in any lizard species. In addition, seasonality affected bacterial composition, and microbial community similarity increased between S. aeneus and S. bicanthalis, as well as between S. grammicus and S. spinosus. Together, our results illustrate that seasonal variation and dietary composition play a role in shaping gut microbiota in lizard populations, but this is not a rule and other ecological factors influence microbiota variation.

Effects of abiotic restoration through rock addition on invertebrate functional diversity in native temperate grasslands

Invertebrates account for over 90% of all described species and provide crucial ecosystem services. Land clearing, including the removal of abiotic habitat features, threatens invertebrate biodiversity, making environmental restoration crucial for conservation. However, little is known about the effects of abiotic restoration compared to the restoration of biotic features. To determine if rock addition increased invertebrate biodiversity, we introduced 120 t of rocks to 10 sites across five grassland reserves in the Australian Capital Territory in a before‐after‐control‐impact design. We sampled invertebrates using pitfall traps before treatment in 2016 and after rock addition in 2019 (during record‐breaking drought). We recorded 29,164 individual invertebrates from 19 orders and undertook a functional trait‐based analysis of rock effects on the invertebrate community. No effects of rock addition were observed on the probability of occurrence, richness, diversity, community similarity, or abundance of any taxonomic or functional group. The abundance of snare‐building spiders and large ants was higher in the control plots at the end of the experiment. These abundance responses in 2019 did not differ from the control or treatment plots in 2016. Thus, some combination of drought and rock addition appears to have neutralized a positive temporal change that was evident without rocks. Despite a regionwide, replicated restoration effort and an extensive functional analysis of invertebrate communities, very little positive response to rock addition was recorded. Rock addition did not have a negative effect on grassland invertebrate biodiversity and may still be beneficial to the long‐term conservation and restoration of vertebrate and invertebrate communities.

Spatial distribution and assembly processes of bacterial communities in riverine and coastal ecosystems of a rapidly urbanizing megacity in China

Rapid urbanization has precipitated significant anthropogenic pollution (nutrients and pathogens) in urban rivers and their receiving systems, which consequentially disrupted the compositions and assembly of bacterial community within these ecosystems. However, there remains scarce information regarding the composition and assembly of both planktonic and benthic bacterial communities as well as pathogen distribution in such environments. In this study, full-length 16S rRNA gene sequencing was conducted to investigate the bacterial community composition, interactions, and assembly processes as well as the distribution of potential pathogens along a riverine-coastal continuum in Shenzhen megacity, China. The results indicated that both riverine and coastal bacterial communities were predominantly composed of Gammaproteobacteria (24.8 ± 12.6 %), Alphaproteobacteria (16.1 ± 9.8 %), and Bacteroidota (14.3 ± 8.6 %), while sedimentary bacterial communities exhibited significantly higher diversity compared to their planktonic counterparts. Bacterial community patterns exhibited significant divergences across different habitats, and a significant distance-decay relationship of bacterial community similarity was particularly observed within the urban river ecosystem. Moreover, the urban river ecosystem displayed a more complex bacterial co-occurrence network than the coastal ecosystem, and a low ratio of negative:positive cohesion suggested the inherent instability of these networks. Homogeneous selection and dispersal limitation emerged as the predominant influences on planktonic and sedimentary bacterial communities, respectively. Pathogenic genera such as Vibrio, Bacteroides, and Acinetobacter, known for their roles in foodborne diseases or wound infection, were also identified. Collectively, these findings provided critical insights into bacterial community dynamics and their implications for ecosystem management and pathogen risk control in riverine and coastal environments impacted by rapid urbanization.

Environmental Flow Increases The Riparian Vegetation Diversity And Community Similarity

Environmental Flow Increases The Riparian Vegetation Diversity And Community Similarity

Distance decay effects predominantly shape spider but not carabid community composition in crop fields in north-western Europe

Agricultural intensification and expansion are regarded as main drivers of biodiversity loss. This conclusion is mainly based on observed declines of local diversity (α-diversity), while effects on community composition homogenization (decrease of β-diversity) at a larger spatial scale are less well understood. Carabid beetles and spiders represent two widespread guilds and are important predators of pest species. Here we surveyed carabid beetles and spiders in 66 winter wheat fields in four northwestern European countries (Germany, the Netherlands, Sweden and UK) and analyzed how their community composition was related to geographic distance (separation distance between any pairwise fields) and three environmental variables: crop yield (proxy for land-use intensity), percentage cropland (proxy for landscape complexity) and soil organic carbon content (proxy for local soil conditions). We further analyzed whether the relationship between carabid beetle and spider community composition and geographic distance was influenced by environmental variables. We found that, 55 % and 75 % of all observed carabid and spider individuals, respectively, belonged to species that occurred in all four countries. However, individuals of species that were unique to a particular country only accounted for 3 % of all collected individuals for both taxa. Furthermore, we found a negative relationship between distance and similarity of spider communities but not for carabid beetle communities. None of the environmental variables were related to similarity of carabid beetle and spider communities, nor moderated the effects of distance. Our study indicates that across a great part of the European continent, arthropod communities (especially carabid beetles) in agricultural landscapes are composed of very similar species that are robust to current variations in environment and land-use.

HME-KG: A method of constructing the human motion encoding knowledge graph based on a hierarchical motion model

The diversity, infinity, and nonuniform description of human motion make it challenging for computers to understand human activities. To explore and reuse captured human motion data, this work defines a more comprehensive hierarchical theoretical model of human motion and proposes a standard human posture encoding scheme. We construct a domain knowledge graph (DKG) named the human motion encoding knowledge graph (HME-KG) based on posture codes and action labels. Community detection, similarity analysis, and centrality analysis are used to explore the potential value of motion data. This paper conducts an evaluation and visualization of HME-KG.

Dynamic and structural response of a multispecies biofilm to environmental perturbations induced by the continuous increase of benzimidazole fungicides in a permeable reactive biobarrier.

This work explores the dynamics of spatiotemporal changes in the taxonomic structure of biofilms and the degradation kinetics of three imidazole group compounds: carbendazim (CBZ), methyl thiophanate (MT), and benomyl (BN) by a multispecies microbial community attached to a fixed bed horizontal tubular reactor (HTR). This bioreactor mimics a permeable reactive biobarrier, which helps prevent the contamination of water bodies by pesticides in agricultural wastewater. To rapidly quantify the microbial response to crescent loading rates of benzimidazole compounds, a gradient system was used to transiently raise the fungicide volumetric loading rates, measuring the structural and functional dynamics response of a microbial community in terms of the volumetric removal rates of the HTR entering pollutants. The loading rate gradient of benzimidazole compounds severely impacts the spatiotemporal taxonomic structure of the HTR biofilm-forming microbial community. Notable differences with the original structure in HTR stable conditions can be noted after three historical contingencies (CBZ, MT, and BN gradient loading rates). It was evidenced that the microbial community did not return to the composition prior to environmental disturbances; however, the functional similarity of microbial communities after steady state reestablishment was observed. The usefulness of the method of gradual delivery of potentially toxic agents for a microbial community immobilized in a tubular biofilm reactor was shown since its functional and structural dynamics were quickly evaluated in response to fungicide composition and concentration changes. The rapid adjustment of the contaminants' removal rates indicates that even with changes in the taxonomic structure of a microbial community, its functional redundancy favors its adjustment to gradual environmental disturbances.

Urbanization alters the geographic patterns of passerine plumage color in China

Urbanization has altered natural landscapes and serves as an environmental filter that selects species with specific traits. Coloration is an important trait associated with biotic interactions and thermoregulation, enabling species’ survival and reproductive success. However, few studies have focused on how species coloration changes in response to urbanization. Here, we used 547 passerine bird species from 42 cities and their corresponding non-urban communities in China to test whether urban species are darker and if they have duller plumage colors than their non-urban counterparts. Furthermore, we examined whether and how urbanization influences avian plumage color homogenization and the extent to which urbanization has altered the strength of the color–latitude geographic pattern in passerine birds across China. We found a 3.2% loss in the coloration space of birds after urbanization, although there were no significant differences in the individual dimensions of colorfulness and lightness between urban and non-urban birds. Avian communities in cities exhibited more plumage color homogenization than those in non-urban communities. There were significant latitudinal gradients in plumage colorfulness and lightness in non-urban communities, but these correlations were weaker in urban communities. Non-urban communities that were more colorful and lighter tended to be duller and darker in urban environments, and vice versa. Our results provide national-scale evidence that urbanization has led to reduced color diversity, increased color-based community similarity, and altered geographic patterns of avian plumage color gradients in China. These findings provide new insights into how rapid human-induced environmental changes have affected animal coloration during the Anthropocene.

Landscape connection and patch complexity explain plant community similarity in sandy grasslands better than habitat amount and landscape heterogeneity via network analysis

Landscape connection and patch complexity explain plant community similarity in sandy grasslands better than habitat amount and landscape heterogeneity via network analysis