Alpha Diversity Patterns Research Articles

Environmental DNA for monitoring the impact of offshore wind farms on fish and invertebrate community structures

AbstractTo reach the renewable energy targets set by the European Commission, a tenfold expansion of the installed offshore wind farms is needed. Since the construction of offshore wind farms may affect local soft‐sediment fauna, an efficient monitoring technique is needed to monitor the potential effects on the marine ecosystem. Here, we assess whether eDNA metabarcoding is a suitable alternative to monitor fish and epibenthos biodiversity in these difficult to access marine habitats. Water sampling and trawl surveys were conducted in parallel in 12 coastal and 18 offshore sites, the latter located inside and outside two offshore wind farms in the Belgian part of the North Sea. 12S eDNA metabarcoding retrieved 85.7% of the fish species caught in the beam trawls, whereas the COI eDNA metabarcoding only identified 31.4% of the epibenthic invertebrate species. Furthermore, the 12S marker resulted in an additional detection of 26 unique fish species, whereas the COI marker detected an additional 90 invertebrate species. Spatial patterns in alpha diversity recovered with eDNA metabarcoding were not significantly different from those observed with morphological determination. Significant differences were found in fish and invertebrate community structures between the coastal, transition and offshore zones as well as on the smaller wind farm scales, which agreed with the morphological beam trawl data. Indicator species found with morphological beam trawl monitoring for each of the three zones (coastal, transition, offshore) were also detected with 12S eDNA metabarcoding, and the latter method detected an additional 31 indicator species. Our findings show the need for adequate quality control of the obtained species lists and reveal that 12S eDNA metabarcoding analyses offers a useful survey tool for the monitoring of fish communities in offshore wind farms, but the used COI assay did not adequately capture the epibenthic communities as observed with beam trawl data.

Molecular and next-generation sequencing analysis of tick-borne pathogens of Rhipicephalus ticks (Acari: Ixodidae) in cattle and dogs

Ticks are small and adaptable arachnid ectoparasites and global carriers of various pathogens that threaten both human and animal health. They are present in many parts of China. A total of 858 ticks were collected from various regions and hosts, then subjected to species identification based on morphological and molecular characteristics, as described in the authors’ previous study. Eighty-three individual tick samples were selected for screening pathogens based on metagenomic next-generation sequencing (mNGS) and polymerase chain reaction (PCR) assays. The genomic DNA of tick species was extracted, and amplification of the bacterial 16S rRNA gene was carried out from DNA of individual ticks using V3-V4 hypervariable regions, before subjecting to metagenomic analysis. Each tick underwent specific PCR tests for identifying the bacterial species present, including Anaplasma, Ehrlichia, Coxiella, and Rickettsia, and also protozoans such as Babesia, Theileria, and Hepatozoon. Illumina NovaSeq sequencing results revealed that the dominant phylum and family in Rhipicephalus spp. were Bacteroidota and Muribaculaceae, respectively. Alpha diversity patterns varied depending on tick sex (R. linnaei only), species and location, but not on host. Furthermore, bacterial pathogens, including A. marginale (58 %, 29/50), A. platys (6 %, 3/50), E. minasensis (2 %, 1/50), Ehrlichia sp. (10 %, 5/50), T. sinensis (24 %, 12/50), T. orientalis (54 %, 27/50) and Coxiella-like bacteria (CLB) (80 %, 40/50) were detected in R. microplus, while E. canis (33.33 %, 10/30), H. canis (20 %, 6/30) and CLB (100 %, 30/30) were detected in R. linnaei. Also, Anaplasma sp. (33.33 %, 1/3), A. marginale (33.33 %, 1/3), R. felis (33.33 %, 1/3) and CLB (100 %, 3/3) were detected in R. haemaphysaloides. Dual and triple co-infections involving pathogens or CLB were detected in 84.00 % of R. microplus, 66.66 % of R. haemaphysaloides, and 33.00 % of R. linnaei. The report on microbial communities and pathogens, which found from Rhipicephalus spp. in Hainan Island, is an important step towards a better understanding of tick-borne disease transmission. This is the first report in the area on the presence of Anaplasma sp., A. marginale, R. felis and Coxiella, in R. haemaphysaloides.

Global mesozooplankton communities show lower connectivity in deep oceanic layers.

Mesozooplankton is a key component of the ocean, regulating global processes such as the carbon pump, and ensuring energy transfer from lower to higher trophic levels. Yet, knowledge on mesozooplankton diversity, distribution and connectivity at global scale is still fragmented. To fill this gap, we applied DNA metabarcoding to mesozooplankton samples collected during the Malaspina-2010 circumnavigation expedition across the Atlantic, Indian and Pacific oceans from the surface to bathypelagic depths. We highlight the still scarce knowledge on global mesozooplankton diversity and identify the Indian Ocean and the deep sea as the oceanic regions with the highest proportion of hidden diversity. We report no consistent alpha-diversity patterns for mesozooplankton at a global scale, neither across vertical nor horizontal gradients. However, beta-diversity analysis suggests horizontal and vertical structuring of mesozooplankton communities mostly attributed to turnover and reveals an increase in mesozooplankton beta-diversity with depth, indicating reduced connectivity at deeper layers. Additionally, we identify a water mass type-mediated structuring of mesozooplankton bathypelagic communities instead of an oceanic basin-mediated as observed at upper layers. This suggests limited dispersal at deep ocean layers, most likely due to weaker currents and lower mixing of water mass types, thus reinforcing the importance of oceanic currents and barriers to dispersal in shaping global plankton communities.

Climate and Environmental Variables Drive Stream Biofilm Bacterial and Fungal Diversity on Tropical Mountainsides.

High mountain freshwater systems are particularly sensitive to the impacts of global warming and relevant environmental changes. Microorganisms contribute substantially to biogeochemical processes, yet their distribution patterns and driving mechanism in alpine streams remain understudied. Here, we examined the bacterial and fungal community compositions in stream biofilm along the elevational gradient of 745-1874 m on Mt. Kilimanjaro and explored their alpha and beta diversity patterns and the underlying environmental drivers. We found that the species richness and evenness monotonically increased towards higher elevations for bacteria, while were non-significant for fungi. However, both bacterial and fungal communities showed consistent elevational distance-decay relationships, i.e., the dissimilarity of assemblage composition increased with greater elevational differences. Bacterial alpha diversity patterns were mainly affected by chemical variables such as total nitrogen and phosphorus, while fungi were affectedby physical variables such as riparian shading and stream width. Notably, climatic variables such as mean annual temperature strongly affected the elevational succession of bacterial and fungal community compositions. Our study is the first exploration of microbial biodiversity and their underlying driving mechanisms for stream ecosystems in tropical alpine regions. Our findings provide insights on the response patterns of tropical aquatic microbial community composition and diversity under climate change.

Comparison of the gut fungal communities among Hooded crane (Grus monacha), Greater white-fronted goose (Anser albifrons), and Bean goose (Anser fabalis) at Shengjin Lake, China

The gut microbes regulate a variety of essential functions in avian hosts. Gut microbes are crucial for understanding avian specie’s ecological role and potential impact on the ecosystem. A wide range of factors shape the gut microbial diversity and communities in avian hosts, including similarity in genotype and shared evolutionary history, particularly in two closely related host species than distinctly related hosts. In this study, high-throughput sequencing methods were applied to compare and study the similarities and differences in the gut fungal communities of two geese from the same genus Anser, Greater white-fronted goose (Anser albifrons, WG), Bean goose (Anser fabalis, BG) with Hooded crane (Grus monacha, HC) sympatric in overlapping niches at Shengjin lake, China. Our findings supported our hypothesis that the two closely related geese shared similar gut fungal alpha diversity patterns compared to Hooded cranes due to similarity in genotype and evolutionary history. In particular, the fungal community composition in the gut of Greater white-fronted goose showed larger variation relative to the other two species. This result suggested that dietary preferences might regulate the gut fungal communities, as Hooded crane and Bean goose share parallel dietary preferences. The results of the abundance null deviation model showed higher values of null deviation (NDV) in Greater white-fronted goose and Bean goose, indicating that the two closely related goose species might be associated with more robust gut filtering for their fungal community relative to Hooded crane species. The fungal co-occurrence networks were complex, with higher stability in the two congeneric geese species relative to Hooded crane. Moreover, 29 animal fungal putative pathogens were identified with high diversity and relative abundance in the two congeneric geese due to their complex migration patterns compared with Hooded cranes. However, due to niche overlap, direct or indirect association may lead to the dissemination of gut microbes among sympatric avian species. These findings have important implications for ecological research, conservation efforts, and wildlife health management. Moreover, these findings illuminate potential ecological and conservation repercussions and increase our understanding of the complex interactions between avian species and their gut flora.

Environmental filtering along a bathymetric gradient: A metabarcoding meta-analysis of free-living nematodes.

Identifying and understanding patterns of biological diversity is crucial at a time when even the most remote and pristine marine ecosystems are threatened by resource exploitation such as deep-seabed mining. Metabarcoding provides the means through which one can perform comprehensive investigations of diversity by examining entire assemblages simultaneously. Nematodes commonly represent the most abundant infaunal metazoan group in marine soft sediments. In this meta-analysis, we compiled all publicly available metabarcoding datasets targeting the 18S rRNA v1-v2 region from sediment samples to conduct a global-scale examination of nematode amplicon sequence variant (ASV) alpha diversity patterns and phylogenetic community structure at different depths and habitats. We found that nematode ASV richness followed a parabolic trend, increasing from the intertidal to the shelf, reaching a maximum in the bathyal and decreasing in the abyssal zone. No depth- or habitat-specific assemblages were identified as a large fraction of genera were shared. Contrastingly, the vast majority of ASVs were unique to each habitat and/or depth zone; genetic diversity was thus highly localized. Overwhelmingly, nematode ASVs in all habitats exhibited phylogenetic clustering, pointing to environmental filtering as the primary force defining community assembly rather than competitive interactions. This finding stresses the importance of habitat preservation for the maintenance of marine nematode diversity.

Unveiling the Ecological Tapestry: Alpha Diversity Patterns in the Banas River Corridor, Gujarat, India

Alpha diversity, also known as α-diversity, refers to the diversity of species within a specific area, community, or ecosystem. In this study, an analysis of alpha diversity in the Banas River corridor of Gujarat was conducted using the quadrate sampling method. The flora of the Banas River corridor in Gujarat demonstrates moderate levels of species diversity, evenness, and richness, indicating a vibrant and diverse ecosystem. Total 133 tree and Shrub species were observed from area. The Shannon diversity index, which measures the variety of plant species present, yielded a value of 2.26. This indicates a reasonable level of species diversity within the area. The Simpson diversity index, which assesses the distribution of individuals among species, resulted in a value of 0.88, suggesting a balanced distribution and promoting a healthy ecosystem. Additionally, the evenness value of 0.92 indicates an equitable representation of species, ensuring that no single species dominates the flora and allowing for the coexistence of multiple species. The Menhinick index, which measures species richness, provided a value of 2.16, indicating a moderate level of species richness in the Banas River corridor. This suggests that the area is home to a diverse range of plant species. Overall, the data from the alpha diversity analysis highlights a diverse and stable ecosystem in the Banas River corridor, characterized by a vibrant mix of plant species. This diversity promotes ecological resilience and the coexistence of different species, contributing to the overall health and functioning of the ecosystem.

DNA metabarcoding on repeat: Sequencing data of marine macrobenthos are reproducible and robust across labs and protocols

DNA metabarcoding can be used in marine environmental monitoring if results are reproducible between labs and robust against modifications to the lab protocol. In this interlaboratory study, we conducted a ring test where subsamples of blended macrobenthos samples were distributed to four laboratories located in Belgium, the Netherlands, Germany and Denmark. Samples were processed by a standardized lab protocol and by an adapted protocol, and the resulting datasets were analyzed with the same bioinformatics pipeline. Different biodiversity indicators were calculated. Our results show that bulkDNA metabarcoding of marine macrobenthos offers a highly reproducible assessment of alpha diversity patterns when using a standardized protocol, since comparable species numbers, Shannon indices and Inverse Simpson indices were found between laboratories. Especially high abundant species and species with large body sizes were shared between the laboratories. The need for using a standardized protocol to enhance comparability in alpha diversity between different studies was shown. Beta diversity patterns are less subjected to changes in the metabarcoding protocol and were almost identical between different laboratories, as the main clustering was always based on the macrobenthic community, independent of the used protocol or the laboratory that conducted the work. We conclude that DNA metabarcoding for marine environmental monitoring is an appropriate method when the aim is to study changes in community patterns and advocate its implementation in routine monitoring programs of national and European authorities, providing that a standardized protocol is implemented and/or a detailed description of the protocol is available.

Diversity Patterns of Vascular Plants at Varied Elevations in Arghakhanchi, West Nepal

The genuine image of biodiversity, as well as their germplasm, is visualized by the turnover of species rather than their similarities in each location. The major goal of this study was to determine the b-diversity pattern of vascular plants growing at 100 m contour elevations and to explore its association with a-diversity and elevation. Primary data were gathered utilizing 4-6 10 x 10 m2 quadrats at 100 m contour elevation, on both the south and north sides, in Arghakhanchi district, west Nepal. Beta diversity represents the change in diversity of species between two communities and is measured by two different matrices: species turnover and similarity. Between two adjacent elevational bands, the species turnover was calculated using the Bray-Curtis dissimilarity index and similarity was assessed using the Jaccard index technique in the Vegan package for R version 4.03. The species richness (a-diversity) and b-diversity indices (Bray-Curtis dissimilarity index and Jaccard similarity index) were regressed by generalized linear model (GLM) method with elevation. The species richness and Jaccard similarity index suggests statistically significant unimodal structure with elevation; however, Bray-Curtis dissimilarity index suggests statistically significant but reverse unimodal pattern. As a result, rather than species turnover, the presence of more related species usually creates the peak area of a unimodal pattern of alpha diversity. The geographical scale of biodiversity loss or its effective preservation by human activities is revealed by beta-diversity. Any region with high beta diversity suggests a wide variety of species, which aids in the administration of conservation programs.

Influence of tick sex and geographic region on the microbiome of Dermacentor variabilis collected from dogs and cats across the United States

As tick-borne diseases continue to increase across North America, current research strives to understand how the tick microbiome may affect pathogen acquisition, maintenance, and transmission. Prior high throughput amplicon-based microbial diversity surveys of the widespread tick Dermacentor variabilis have suggested that life stage, sex, and geographic region may influence the composition of the tick microbiome. Here, adult D. variabilis ticks (n = 145) were collected from dogs and cats from 32 states with specimens originating from all four regions of the United States (West, Midwest, South, and Northeast), and the tick microbiome was examined via V4-16S rRNA gene amplification and Illumina sequencing. A total of 481,246 bacterial sequences were obtained (median 2924 per sample, range 399–11,990). Fifty genera represented the majority (>80%) of the sequences detected, with the genera Allofrancisella and Francisella being the most abundant. Further, 97%, 23%, and 5.5% of the ticks contained sequences belonging to Francisella spp., Rickettsia spp., and Coxiella spp., respectively. No Ehrlichia spp. or Anaplasma spp. were identified. Co-occurrence analysis, by way of correlation coefficients, between the top 50 most abundant genera demonstrated five strong positive and no strong negative correlation relationships. Geographic region had a consistent effect on species richness with ticks from the Northeast having a significantly greater level of richness. Alpha diversity patterns were dependent on tick sex, with males exhibiting higher levels of diversity, and geographical region, with higher level of diversity observed in ticks obtained from the Northeast, but not on tick host. Community structure, or beta diversity, of tick microbiome was impacted by tick sex and geographic location, with microbiomes of ticks from the western US exhibiting a distinct community structure when compared to those from the other three regions (Northeast, South, and Midwest). In total, LEfSe (Linear discriminant analysis Effect Size) identified 18 specific genera driving these observed patterns of diversity and community structure. Collectively, these findings highlight the differences in bacterial diversity of D. variabilis across the US and supports the interpretation that tick sex and geographic region affects microbiome composition across a broad sampling distribution.

Bacterial and Protistan Community Variation across the Changjiang Estuary to the Ocean with Multiple Environmental Gradients.

Plankton microorganisms play central roles in the marine food web and global biogeochemical cycles, while their distribution and abundance are affected by environmental variables. The determinants of microbial community composition and diversity in estuaries and surrounding waters with multiple environmental gradients at a fine scale remain largely unclear. Here, we investigated bacterial and protistan community assembly in surface waters from 27 stations across the Changjiang Estuary to the ocean, with salinity ranging from 0 to 32.1, using 16S rRNA and 18S rRNA gene amplicon sequencing. Statistical analyses revealed that salinity is the major factor structuring both bacterial and protistan communities. Salinity also acted as a significant environmental determinant influencing alpha-diversity patterns. Alpha diversity indices for bacterial and protistan communities revealed a species minimum in higher-salinity waters (22.1–32.1). Contrary to the protistan community, the highest bacterial diversity was identified in medium-salinity waters (2.8–18.8), contrasting Remane’s Artenminimum concept. The distribution of major planktonic taxa followed the expected pattern, and the salinity boundary for Syndiniales was specifically identified. These findings revealed the significant effects of salinity on the microbial community across an estuary to ocean transect and the distinct response to salinity between bacterial and protistan communities.

Species misidentification affects biodiversity metrics: Dealing with this issue using the new R package naturaList

Biodiversity databases are increasingly available and have fostered accelerated advances in many disciplines within ecology and evolution. However, the quality of the evidence generated depends critically on the quality of the input data, and species misidentifications are present in virtually any occurrence dataset. Yet, the lack of automatized tools makes the assessment of the quality of species identification in big datasets time-consuming, which often induces researchers to assume that all species are reliably identified. In this study, we address this issue by evaluating how species misidentification can impact our ability to capture ecological patterns, and by presenting an R package, called naturaList, designed to classify species occurrence data according to identification reliability. naturaList allows the classification of species occurrences up to six confidence levels, in which the highest level is assigned to records identified by specialists. We obtained a list of specialists by using the species occurrence dataset itself, based on the identifier names within it, and by entering an independent list, obtained by contacting experts. Further, we evaluate the effects of filtering out occurrence records not identified by specialists on the estimations of species niche and diversity patterns. We used the tribe Myrteae (Myrtaceae) as a study model, which is a species-rich group in Central and South America and with challenging taxonomy. We found a significant change in species niche in 13% of species when using only occurrences identified by specialists. We found changes in patterns of alpha diversity in four genera and changes in beta diversity in all genera analyzed. We show how the uncertainty in species identification in occurrence datasets affects conclusions on macroecological patterns by generating bias or noise in different aspects of macroecological patterns (niche, alpha, and beta diversity). Therefore, to guarantee reliability in species identification in big data sets we recommend the use of automated tools such as the naturaList package, especially when analyzing variation in species composition. This study also represents a step forward to increasing the quality of large-scale studies that rely on species occurrence data.

Community metabarcoding reveals the relative role of environmental filtering and spatial processes in metacommunity dynamics of soil microarthropods across a mosaic of montane forests.

Disentangling the relative role of environmental filtering and spatial processes in driving metacommunity structure across mountainous regions remains challenging, as the way we quantify spatial connectivity in topographically and environmentally heterogeneous landscapes can influence our perception of which process predominates. More empirical data sets are required to account for taxon- and context-dependency, but relevant research in understudied areas is often compromised by the taxonomic impediment. Here we used haplotype-level community DNA metabarcoding, enabled by stringent filtering of amplicon sequence variants (ASVs), to characterize metacommunity structure of soil microarthropod assemblages across a mosaic of five forest habitats on the Troodos mountain range in Cyprus. We found similar β diversity patterns at ASV and species (OTU, operational taxonomic unit) levels, which pointed to a primary role of habitat filtering resulting in the existence of largely distinct metacommunities linked to different forest types. Within-habitat turnover was correlated to topoclimatic heterogeneity, again emphasizing the role of environmental filtering. However, when integrating landscape matrix information for the highly fragmented Quercus alnifolia habitat, we also detected a major role of spatial isolation determined by patch connectivity, indicating that stochastic and niche-based processes synergistically govern community assembly. Alpha diversity patterns varied between ASV and OTU levels, with OTU richness decreasing with elevation and ASV richness following a longitudinal gradient, potentially reflecting a decline of genetic diversity eastwards due to historical pressures. Our study demonstrates the utility of haplotype-level community metabarcoding for characterizing metacommunity structure of complex assemblages and improving our understanding of biodiversity dynamics across mountainous landscapes worldwide.

Recovery of temporary pond alpha and beta diversity after wildfire disturbance: the role of dispersal and recolonization processes

ABSTRACT Wildfires are a global disturbance being enhanced by human-induced pressures. Their frequency and intensity are expected to increase in the near future in regions such as the Mediterranean Basin. While responses of terrestrial systems to wildfire have been thoroughly studied, aquatic systems such as temporary ponds have received less attention. Furthermore, previous works have focused on wildfire impacts in aquatic systems from a functional and trait-based approach, but such disturbances can also impact the diversity of these systems at the local and regional level. In this work, we assessed wildfire impacts on alpha and beta diversity of Mediterranean temporary ponds by analysing samples of pond macrofauna after a wildfire burned part of a cluster of these habitats. The wildfire did not change alpha diversity patterns, but differences in beta diversity were observed when considering species abundance. Species with greater contribution to beta diversity were more strongly represented in unburned ponds after the wildfire. These changes occurred mostly during the beginning of the hydroperiod, which increased regional differences in burned ponds, but decreased toward the middle and the end of the hydroperiod. Overall, we report a fast recovery of communities after the wildfire, tightly linked to a rapid recolonization that increased similarity. Landscape structure and seasonal succession are key to the recovery of these systems. However, this recovery capacity might be compromised in the future by increasing occurrence of wildfire and the potential for substantial habitat loss.

Neurodevelopment correlates with gut microbiota in a cross-sectional analysis of children at 3\xa0years of age in rural China

We investigated cross-sectional associations between children’s neurodevelopment and their gut microbiota composition. Study children (36 months of age) lived in rural China (n = 46). Neurodevelopment was assessed using the Bayley Scales of Infant Development, 2nd Edition, yielding the Mental Developmental Index (MDI) and Psychomotor Developmental Index (PDI). Children's gut microbiota was assessed using 16S rRNA gene profiling. Microbial diversity was characterized using alpha diversity patterns. Additionally, 3 coabundance factors were determined for the 25 most abundant taxa. Multivariable linear regression models were constructed to examine the relationships between Bayley scores (MDI and PDI) and children's gut microbiota. In adjusted models, MDI and PDI scores were not associated with alpha diversity indices. However, in adjusted models, MDI and PDI scores were positively associated with the first coabundance factor, which captured positive loadings for the genera Faecalibacterium, Sutterella, and Clostridium cluster XIVa. For an interquartile range increase in the first coabundance factor, MDI scores increased by 3.9 points [95% confidence interval (CI): 0, 7.7], while PDI scores increased by 8.6 points (95% CI 3.1, 14). Our results highlight the potential for gut microbial compositional characteristics to be important correlates of children's Bayley Scales performance at 36 months of age.

Exploring the potential of metabarcoding to disentangle macroinvertebrate community dynamics in intermittent streams

Taxonomic sufficiency represents the level of taxonomic detail needed to detect ecological patterns to a level that match the requirement of a study. Most bioassessments apply the taxonomic sufficiency concept and assign specimens to the family or genus level given time constraints and the difficulty to correctly identify species. This holds particularly true for stream invertebrates because small and morphologically similar larvae are hard to distinguish. Low taxonomic resolution may hinder detecting true community dynamics, which thus leads to incorrect inferences about community assembly processes. DNA metabarcoding is a new, affordable and cost-effective tool for the identification of multiple species from bulk samples of organisms. As it provides high taxonomic resolution, it can be used to compare results obtained from different identification levels. Measuring the effect of taxonomic resolution on the detection of community dynamics is especially interesting in extreme ecosystems like intermittent streams to test if species at intermittent sites are subsets of those from perennial sources or if independently recruiting taxa exist. Here we aimed to compare the performance of morphological identification and metabarcoding to detect macroinvertebrate community dynamics in the Trebbia River (Italy). Macroinvertebrates were collected from four perennial and two intermittent sites two months after flow resumption and before the next dry phase. The identification level ranged from family to haplotype. Metabarcoding and morphological identifications found similar alpha diversity patterns when looking at family and mixed taxonomic levels. Increasing taxonomic resolution with metabarcoding revealed a strong partitioning of beta diversity in nestedness and turnover components. At flow resumption, beta diversity at intermittent sites was dominated by nestedness when family-level information was employed, while turnover was evidenced as the most important component when using Operational Taxonomic Units (OTUs) or haplotypes. The increased taxonomic resolution with metabarcoding allowed us to detect species adapted to deal with intermittency, like the chironomidCricotopus bicinctusand the ephemeropteranCloeon dipterum. Our study thus shows that family and mixed taxonomic level are not sufficient to detect all aspects of macroinvertebrate community dynamics. High taxonomic resolution is especially important for intermittent streams where accurate information about species-specific habitat preference is needed to interpret diversity patterns induced by drying and the nestedness/turnover components of beta diversity are of interest to understand community assembly processes.

The first botanical explorations of bryophyte diversity in the Brazilian Amazon mountains: high species diversity, low endemism, and low similarity

We investigated the species richness, endemism, and similarity of the bryoflora (mosses and liverworts) on five Brazilian Amazon mountains (four Tepuis and one rocky outcrop), to determine the floristic relationships between them using presence/absence matrix. Cluster analysis based on the Jaccard index was used to determine similarities between the plant assemblages in five areas. We also performed a principal component analysis to determine which abiotic variables best explained the variations between those mountains. We surveyed the bryophyte species on each of the five mountains to identify the diversity of mosses and liverworts and to answer to the following questions: (1) How many bryophyte species are there in total area (gama diversity) and on each mountain (alpha diversity)? (2) Do mosses and liverworts share patterns of diversity? (3) Can patterns of alpha diversity be used to predict patterns of beta diversity? (4) What are the species distribution patterns? (5) How many endemic species are there in the mountains? and, (6) Is there high similarity among those bryophyte floras? We encountered 425 species, 144 genera, and 51 families of bryophytes, with Lejeuneaceae and Lepidoziaceae being the richest families. A considerable number of floristic novelties were encountered: 18 species new to Brazil; 39 species new to northern Brazil; 21 species new to Amazonas State; and 2 species new to science and only recently described. Over 43% of the bryophytes have a tropical America distribution, approximately 7% are Pantropical, 6.5% are Afro-American, and 3% are endemic to Brazil (6 liverworts and 6 mosses), and 6% are widespread globally. We present a checklist of 425 bryophyte species (144 genera and 51 families) of which 12 are endemic. Patterns of endemism of the bryophyte flora on the Tepuis differ from those exhibited by angiosperms (in the latter three times higher). Thirty-nine of these species were new for the Amazonia domain in Brazil, increasing by 7% the previous total of Amazonian recorded species. The similarity between sites was low, ranging from 3 to 25%. PCA analysis showed temperature variables explaining the greater part of the variance (76.6%) between the mountains. Our results demonstrate that patterns of alpha diversity cannot be used to predict patterns of beta diversity. This paper represents the first evaluation of bryophytes on five Brazilian Amazon mountains, giving insight into their species richness, endemism, and similarity, and providing baseline information for analyzing species’ turnover rates, migration, invasion events, etc. These results also represent an increase in our general knowledge of the Brazilian bryoflora and are relevant to the conservation of bryophyte diversity in the Amazon forest, and represent a contribution toward the targets of the Global Strategy for Plant Conservation.

Diversity of epiphyte ferns along an elevational gradient in El Triunfo Biosphere Reserve, southern Mexico

Background and aims – In the tropics, some studies have found that the richness of epiphytic ferns present a peak at mountain mid-elevations. However, it is not well understood how transitions from tropical to subtropical conditions affect this peak, and even less is known about beta diversity of epiphytic ferns. Thus, the objective is to understand the effect of climatic gradients on the variation of local richness of ferns and beta diversity patterns along an elevational gradient in a mountain system in southern Mexico.Methods – We sampled 32 trees, each in four elevational bands (100–2200 m). Alpha diversity patterns were analysed using linear regression models. We used the Morisita index to quantify species turnover between bands. An additive partitioning approach was used to analyse the degree to which individual trees, plots, and bands contributed to total species richness. We evaluated the influence of climatic variables on species composition via linear regression models.Key results – A total of 30 species in five families were recorded. Each family contributed in different magnitude to the elevational richness pattern, with Polypodiaceae dominating due to its richness and presence along the entire transect. Alpha diversity at the three scales (αtree, αplot, αband) increased with elevation and rainfall, and with decreasing temperature. Species turnover was high along the gradient, but was scale-dependent, with βtransect (65–75%) and βband (14%) with the greatest contributing to total diversity. Although the contribution of the individual trees was lower, it increased with elevation. Conclusions – We emphasize the importance of including different scale levels in analyses of diversity along elevational gradients. In the region, cloud forest on the mountain peaks harbours the highest diversity of epiphytic fern communities. Due to a limited extent of this mountain range, the epiphyte ferns are susceptible to the effects of climate change.

Biodiversity associations of soil fauna and plants depend on plant life form and are accounted for by rare taxa along an elevational gradient

Biodiversity interactions between aboveground and belowground biota have been a central focus of ecology in recent years, particularly in the context of environmental change. However, few studies have systematically assessed the biodiversity relationships of plants and soil fauna from rare to abundant taxa along environmental gradients, especially in the rhizosphere. This study aimed at exploring the alpha and beta diversity associations between plants and soil fauna along an elevational gradient while systematically considering rare to abundant plants and animals, and different plant life forms. We sampled soil fauna (litter fauna and rhizosphere fauna of trees, shrubs and herbs) and investigated plant diversity in 119 plots along an elevational gradient (from 1,020 to 1,770 asl) on Dongling Mountain, China. We calculated alpha diversity from both Rényi's generalized entropy function and Jost's effective species numbers assigning different weights to abundant and rare taxa. Beta diversity was obtained based on a presence–absence metric (beta-sim) and an abundance-based metric (beta-morisita). Abundant litter fauna showed decreasing alpha diversity patterns with increasing elevation, whereas rare litter fauna showed hump-shaped patterns. Abundant litter fauna diversity was positively correlated with abundant tree diversity, but rare litter fauna were negatively correlated with abundant shrub diversity. The diversity of rare fauna associated with the herb rhizosphere showed hump-shaped elevational patterns, whereas no patterns were found for abundant fauna associated with the herb rhizosphere. Rare fauna diversity associated with the herb rhizosphere was negatively correlated with rare herb diversity. No beta diversity correlations between rhizosphere fauna and plants were detected, whereas the beta-sim diversity of litter fauna was positively correlated with that of trees and herbs. Our study suggests that litter fauna are more closely coupled with plant diversity than rhizosphere fauna. We conclude that the diversity associations of plants and soil fauna are dependent on plant life form and are largely driven by rare taxa. Furthering this understanding will enhance our ability to predict the responses of belowground communities to environmental change based on information of plant communities.

Oceanic Microplankton Do Not Adhere to the Latitudinal Diversity Gradient.

A latitudinal biodiversity gradient has captivated ecologists for years, and has become a widely recognized pattern in biogeography, manifest as an increase in biodiversity from the poles to the tropics. Oceanographers have attempted to discern whether these distribution patterns are shared with marine biota, and a lively debate has emerged concerning the global distribution of microbes. Limitations in sampling resolution for such large-scale assessments have often prohibited definitive conclusions. We evaluated microbial planktonic communities along a ~ 15,400-km Pacific Ocean transect with DNA from samples acquired every 2 degrees of latitude within a 3-month period between late August and early November 2003. Next-generation sequencing targeting the Bacteria, Archaea, and Eukarya yielded ~ 10.8 million high-quality sequences. Beta-analysis revealed geographic patterns of microbial communities, primarily the Bacteria and Archaea domains. None of the domains exhibited a unimodal pattern of alpha-diversity with respect to latitude. Bacteria communities increased in richness from Arctic to Antarctic waters, whereas Archaea and Eukarya communities showed no latitudinal or polar trends. Based on our analyses, environmental factors related to latitude thought to influence various macrofauna may not define microplankton diversity patterns of richness in the global ocean.