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• Optimal sampling resolution of eDNA-based fish monitoring needs refinement. • We empirically assessed sampling intensity at multiple scales in three rivers. • Downstream eDNA transport facilitates species detection versus electrofishing. • Include upstream sites to capture diverse habitats and environmental factors. • Key sampling site locations vary minimally within small-scale transects. Effective conservation management of river systems requires a comprehensive understanding of local and regional biodiversity, necessitating accurate characterization of species communities. Environmental DNA (eDNA) metabarcoding has emerged as a pivotal tool for assessing aquatic organisms, especially fish communities. However, optimal sampling resolution and site positioning to obtain robust fish diversity indices across heterogeneous river systems remain inadequately understood. This study empirically evaluates the optimal number of eDNA samples needed to accurately capture diversity both locally and stream-wide across three distinct river systems, comparing eDNA metabarcoding results to traditional electrofishing data. Habitat and landscape factors were characterized to interpret the localisation of key sampling sites contributing most to the overall species richness. We detected 30 fish species via eDNA metabarcoding, compared to 28 species by electrofishing, with eDNA requiring fewer sampling sites per river system. To reach ≥ 95 % of the estimated species richness, eDNA analyses required between one and nine sites across three river systems spanning ten kilometres each. In the most diverse river, a single eDNA sampling site even achieved a higher species richness (n = 20 species) compared to the nine required sites to reach ≥ 95 % of the estimated species richness via electrofishing (n = 9 species). To account for eDNA particle dilution and degradation over larger distances (>1 km), sampling at both upstream and downstream sites may be crucial, with strategic site selection further refined by factors like adjacent stream inflows, substrate type, and river discharge rate, all of which influence species-specific habitat occupancy. On a smaller scale, the location of key sampling sites only moderately differs within 100-meter transects therewith informing on the precise placement of those sampling sites. Our work highlights the robustness and cost-effectiveness of eDNA analyses for riverine biodiversity assessment, demonstrating strong potential for enhancing various conservation practices. [ABSTRACT FROM AUTHOR]

Fire modifies the composition and distribution of biodiversity, but the availability of broad elevational gradients for evaluating its effects is limited. Studies conducted along elevational gradients provide valuable insights into the impacts of large-scale disturbances. Due to their sensitivity to environmental changes and low palatability to invasive herbivores, bryophytes serve as effective bioindicators for analyzing disturbance levels in oceanic island ecosystems where herbivores have been introduced. Our research focused on examining how α and β diversity and bryophyte species composition change along an elevational gradient from 200 to 2000 m a.s.l. in areas affected by fire 20 years ago compared to control areas that have been fire-free for at least 50 years. This study was carried out using different functional bryophyte groups in the pine forest of La Palma Island (Canary Islands), where this ecosystem is well represented. The findings revealed the sensitivity of the Canarian pine forest ecosystem to fire. Pine forest areas burnt 20 years ago were significantly poorer in bryophyte species than those in areas free from fire for at least 50 years. α-diversity is proposed as the most indicative parameter for analyzing the impacts of fire on the studied functional groups along the entire gradient analyses. However, β-diversity is more dependent on environmental conditions, increasing in the wettest pine forests. The results suggest that the fire impacts vary depending on the specific functional group of bryophytes and the type of pine forest. • Bryophyte functional groups' responses to fire are studied in Canarian pine forests. • Fire modifies the richness, cover, diversity, and species composition of bryophytes. • Fire effects vary along the elevational gradient according to each functional group. • α-diversity is the most indicative parameter for analyzing the impacts of fire. • β-diversity is highly dependent on moisture, increasing in the wettest areas. [ABSTRACT FROM AUTHOR]

This paper continues the studies on the role of bacteria in the environment of summer truffle (Tuber aestivum), focusing on ascomata at three sites in the Nida Basin (southern Poland). Bacterial taxa and the number of OTU sequences identified were determined based on analysis of peridium and gleba collected in 2017 and 2018. The aim of the presented work is to learn the structure of bacterial communities associated with the ascomata of the summer truffle T. aestivum forming in specific stands in south Poland and fine roots of surrounding trees. Sanger DNA sequencing, and next-generation sequencing (NGS) were used. NGS sequencing platforms short-read (300 bases) was selected, using a MiSeq Illumina. The Kruskall-Wallis test was used for alpha diversity analysis and the PERMANOVA test for beta diversity. Alpha and beta biodiversity analyzes were performed using various indices (Chao1, Simpson, Shannon, Faith's phylogenetic, observed OTUs, Heip's evenness measure - alpha diversity; UniFrac, Jaccard, Bray–Curtis - beta diversity). The Sanger method identified six bacterial taxa that were dominant in the community: Bacillus (86.7 %), Pseudomonas (51.5 %), Stenotrophomonas (15.5 %), Paenibacillus (7.9 %), Rhizobium (7.3 %), and Chryseobacterium (8.5 %). In contrast, NGS results showed the dominance (at OTUs >10,000) of taxa: Bradyrhizobiaceae, Sphingobacteriaceae, Micrococcaceae, Yersiniaceae, Sphingomonadaceae, Rhizobiaceae, Flavobacteriaceae, and Comamonadaceae. The PERMANOVA test for the Bray-Curtis and Jaccard indices showed dissimilarities between samples from two of the sites with respect to beta diversity. Significant differences were found in the bacterial communities colonizing the ascomata of T. aestivum and in the root communities with T. aestivum ectomycorrhizae the purpose of this study. The results obtained may be helpful in selecting and monitoring sites suitable for the formation of ascomata of T. aestivum. [ABSTRACT FROM AUTHOR]

Decline in tree species diversity is a widespread trend in eastern US forests, with implications for ecosystem functions and services, biodiversity and vulnerability to climate change and other stressors. While some impacts on diversity are widespread such as forest pests, forest management practices vary across the landscape. For example, forests in US national parks are managed to promote ecological integrity, develop under natural disturbance regimes, and are largely protected from timber harvesting. In this study we compared forests in 39 eastern US national parks with surrounding matrix forests to assess whether forest protection has led to differences in tree diversity patterns in parks. We calculated multiple alpha and beta diversity metrics using tree stem data. We examined alpha diversity metrics at the scale of the 7.31 m radius subplot and for an equal number of individuals, and examined beta diversity at multiple scales. This is the first study to compare tree diversity in protected lands with the surrounding forest matrix over such a large area of the US, and is only possible because of the 10+ years of data that are publicly available from US Forest Service (USFS) Forest Inventory and Analysis (FIA) and the National Park Service (NPS) Inventory and Monitoring (I&M) programs. Overall, results indicated that park forests have consistently greater alpha diversity. Park forests have higher tree species richness, particularly after the influence of the number of individuals was removed. Park forests also consistently had higher Shannon Evenness, lower McNaughton Dominance, and higher percentage of rare species. Beta diversity analyses also suggest that parks were less homogenous across sites, although results are exploratory due to differences in scale and small sample size. While a number of studies have documented higher diversity in protected areas, few studies have examined multiple diversity metrics or covered the large area of our study. Combining these results with a previous study, which found parks to have consistently greater structural complexity than surrounding forests, park forests may respond differently and potentially be more resilient to climate change and other stressors than unprotected forests, as there is a greater chance that some of the tree species or size cohorts present will persist through climate change. Continued monitoring is important to determine how forests respond to climate change and other stressors, and whether specific management actions, such as protecting more forests, translocating species, or altering management practices, are necessary to maintain forest biodiversity and function. [ABSTRACT FROM AUTHOR]

Mammals play innumerous ecological functions in terrestrial ecosystems and are in decline in the Atlantic Forest. Using a biogeography approach with tools to analyze metacommunities, this study aimed to understand how mammal diversity would vary spatiotemporally across the Atlantic Forest. Secondary data about mammal communities was obtained using search engines. A nestedness analysis and spatial autocorrelations were used to evaluate the spatial patterns of richness. Metacommunity models were used based on species-neutral diversity to measure partitioning and estimate and compare diversity at different spatial and temporal scales, and regression models were made to evaluate the diversity variation obtained in relation to biogeographical predictors. The richness of mammals had intermediary nestedness and a spatial autocorrelation. We obtained high beta diversity for the entire Atlantic Forest, which was similar to simulated values and decreased at smaller spatial and temporal scales. The diversity of medium- to large-bodied mammals along the Atlantic Forest is composed of a nested summary of local to regional diversities, yet the tropical region was very important to the composition of the overall diversity. The different multiscale approaches and results may contribute to better understanding the diversity of medium- to large-bodied mammal communities and how they vary in the Atlantic Forest. Both the neutral paradigm and other metacommunity paradigms have complementary strengths in species diversity at several scales. We conclude that conservation strategies should consider all scales in the Atlantic Forest, because the diversity of mammals is dependent both the local and regional pool of mammals. Some of the most important standing issues are to find out whether dispersal across regional landscapes occurs for most species and, if it does, to ensure that this is maintained or increased, to maintain species diversity and ecological processes. [ABSTRACT FROM AUTHOR]

[Display omitted] • Patterns and driving factors of fish biodiversity in metacommunities were quantified. • Almost all indices of alpha and beta diversity decreased during the 1980 s-2010 s. • Land use contributed more to biodiversity decline than other stressors. Understanding patterns and driving factors of freshwater fish biodiversity in metacommunities is essential for biological conservation but rarely studied in regions experiencing rapid land use changes. We examined changes of both alpha and beta fish diversities in taxonomic, functional, and phylogenetic facets during the 1980 s to 2010 s, and quantified contributions from natural and human drivers in lakes located in China's fastest economic development region. Results showed that almost all indices of alpha and beta diversity decreased through time. For alpha diversity, taxonomic and functional richness declined by 13 to 15%. Rheophilic and piscivorous fish species declined by 50 and 36%, respectively. For beta diversity, the decline of overall functional (-31%) diversity was greater than taxonomic (-17%) and phylogenetic (-19%) diversity. The decline of multiple facets of beta diversity indicated that fish communities in these lakes have homogenized through time. Land use (i.e., increased urban land and aquaculture ponds), hydrology (i.e., increased water level), climate (i.e., increased air temperature), and fishing (i.e., increased lake fishery catch) factors all made significant contributions to both alpha and beta fish diversity decline in multiple facets. The overall contribution from land use to the decline of multidimensional fish diversity was greater than those of other stressors. While attention should be given to both local human disturbance and regional climate factors, in regions experiencing rapid economic development and land use changes, local disturbances should be considered as a priority in biodiversity management plans. [ABSTRACT FROM AUTHOR]

• Minor road redevelopment affects the alpha and beta diversity of bird communities. • Functional diversity is the most sensitive index to minor road redevelopment. • The negative impacts were weaker than that of continuous-use roads. • Minor road redevelopment negatively affected the recovery process of avian diversity. • Even minor road redevelopment warrants careful environmental impact assessment. Although the effects of major roads and highways on biodiversity have received considerable attention, there is a lack of research considering how smaller and less-used roads might also impact wildlife, especially during the initial re-used development phase of abandoned roads, despite these minor roads being much more extensive and pervasive. Here, we examined how even minor redevelopment of former-abandoned logging roads can impact bird community alpha and beta diversity indices at the taxonomic, functional, and phylogenetic levels in a biodiversity conservation hotspot in central China. The minor redevelopment (i.e., re-paved) of former-abandoned roads generally reduced bird alpha and beta diversity compared to undeveloped abandoned roads, especially at the functional level. Compared with continuous-use roads, minor road redevelopment shows only a slight impact on avian diversity. Notably, compared to old-growth forest reference stands and undeveloped abandoned roads, minor road redevelopments have negative effects on the recovery process of avian diversity. Furthermore, the structure and composition of the high tree layer significantly affected avian functional and phylogenetic diversity, and low shrub layer vegetation mainly influenced taxonomic and phylogenetic diversity. To mitigate the effects of minor forest logging roads on avian biodiversity in priority biodiversity conservation areas, we propose the following: (1) roads that have fallen into disuse should be allowed and encouraged to re-naturalise; (2) roads should only be paved, and cleared back as strictly necessary, allowing grassy or gravel roads to suffice where possible; and (3) if road development is necessary, key umbrella tree species should be planted deliberately to support maximal community diversity and to maintain ecosystem functions and processes. [ABSTRACT FROM AUTHOR]

In agriculture-dominated landscapes, agricultural intensification and associated landscape homogenization have caused large declines in farmland biodiversity. This study was aimed at determining how agricultural landscape composition drives community diversity and composition of farmland birds in the characteristic bocage landscape in Brittany (NW France) on a broad scale. Using bird atlas data from the region (2004–2008; 10 × 10 km), we analyzed the importance of different components of agricultural landscape composition (types of crops, amount of semi-natural covers and elements, and artificial lands) on the alpha diversity and beta diversity of farmland birds of different functional groups, defined depending on the degree of farmland specialization and ecological requirements. Agricultural landscape composition features explained a small amount of variation in alpha and beta diversity, particularly for specialists and residents. Cereal crops were negatively correlated with alpha diversity of all the functional groups considered whereas rotational grasslands were negatively associated with migrant and insectivorous alpha diversity. Although shrublands are not common in Brittany, they were positively associated with the occurrence of some species and particularly with alpha diversity of all the functional groups but specialists and residents. At the spatial grain of analysis, community composition was mainly driven by a gradient of alteration of the bocage . To conclude, we claim for the consideration of regional idiosyncrasies in far-reaching planning schemes to prevent future biodiversity loss in agriculture-dominated landscapes due to agricultural intensification. In view of the observed large-scale trends gathered from atlas data analysis and the small amount of explained variation, we also advocate for subsequent finer scale bespoke surveys to determine the biodiversity status associated with the valuable bocage agricultural landscape. [ABSTRACT FROM AUTHOR]

Abstract: Cacti are important elements of the flora in many ecosystems of the Americas. However, the factors that determine their richness and composition are not well known, particularly at the regional scale. The aim of this work was to study the patterns of cactus richness (both species and growth forms) and composition in the Sierras del Norte mountain range (Córdoba Province, Argentina). Species presence was recorded at 55 sites covering an altitudinal gradient from 203 to 970m. Twenty four species from eight genera were recorded in the area. Total species richness and growth form richness decreased with increasing altitude. The richness of columnar and short columnar species decreased with increasing altitude, whereas richness of globose species increased. Opuntioid richness did not respond to altitude. Species composition was strongly related to altitude. Gymnocalycium bruchii and Parodia erinacea occurred at sites located at higher altitudes, whereas at sites at lower altitudes, Gymnocalycium schickendantzii, Stetsonia coryne and Cleistocactus baumannii, among other species, were present. Our results highlight the importance of altitude in shaping the distribution of species and growth forms in the Sierras del Norte Mountains. [Copyright &y& Elsevier]

Abstract: Progress in understanding the patterns of plant diversity requires a conceptualization and quantification of the hierarchy of patch configuration that exists in plant communities across levels of observation. In order to identify the scales at which vascular plant diversity is maximized, we investigated the hierarchical organization of understory vascular plant diversity in relation to canopy patch types in mature boreal mixedwood forests in western Canada. In each of two study areas within a 30km2 landscape (55° N, 112° E) we sampled four canopy patch types: conifer, mixed conifer-broadleaf, broadleaf and canopy gaps. Understory diversity (richness and Shannon’s (H′) index) was additively partitioned in relation to these four canopy patch types across a hierarchy of four scales; α-individual patch +β1-among patches within canopy patch type +β2-among canopy patch types within area +β3-between areas. We also examined understory species abundance patterns by means of rank-abundance plots fitted to relative abundance models. The largest partition of species richness was among patches within canopy patch type (β1). For Shannon diversity index, the largest partition was at the within-individual patch level (α1) indicating that evenness was high at the patch level but that dominance increased at higher levels in the hierarchy. The assessment of relative abundance by means of rank abundance plots suggested that the canopy patch types differed in terms of the ecological mechanisms influencing diversity patterns. Considering plant diversity within a hierarchical framework is critical for the understanding and management of biodiversity as maximum levels of plant richness and evenness do not necessarily occur at the same observational scales. Management practices which retain the natural hierarchies of vegetation patches will help conserve plant community richness and diversity. [Copyright &y& Elsevier]

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We analyze the impact of grazing on dung beetle diversity at the Barranca de Metztitlán Biosphere Reserve, a xeric ecosystem in central Mexico with a long history of use by humans. We compared the community structure, as well as the alpha and beta diversity between two cover conditions (open and closed vegetation) that represent the impact of grazing within a habitat, and between habitat types (submountainous and crassicaule scrublands). From 576 samples we collected 75,605 dung beetles belonging to 20 taxa. While mean species richness and diversity were different between habitat types, cumulative species richness was not. The effects of grazing on vegetation structure influenced the cumulative species richness and diversity of dung beetles in the submountainous scrubland, where grazing has created land mosaics of a grassland matrix with scrubland patches. This was not the case in the crassicaule scrubland where the impact of grazing is not as evident. Beta diversity significantly responds to the effects of grazing on habitat conditions. We discuss the ecological factors that may promote these responses by landscape diversity components. We also identify the species that could act as useful indicators to monitor the effect of land management on biodiversity. Our results indicate cattle farming maintains a diversified land mosaic, and these areas support more diverse dung beetle ensembles than homogeneous areas of closed, shrubby vegetation cover. Thus, controlled grazing activity could certainly favour the conservation of dung beetle biodiversity and improve ecosystem functioning by maintaining dung decomposition rates. [Copyright &y& Elsevier]

Abstract: Differences in alpha and beta bat diversity among montane rainforest and five shaded coffee plantations under different management regimes, as well as some environmental factors and vegetation parameters influencing bat richness, were evaluated for the first time in southeastern Chiapas, Mexico. In each site, bats were captured every 2 months from March 2004 to July 2005, with six mist-nets, during two nights, using the capture–recapture method. We captured 2970 individuals of 43 bat species. Montane rainforest had the greatest alpha diversity (H′=2.681; n =37), whereas alpha diversity was similar among coffee plantations (H′=2.229–2.364; n =23–26). The number of frugivorous and nectarivorous species was similar among the sites; the greatest exchange in species composition (beta diversity) occurred for insectivorous bats, which reduce their number in coffee plantations as pesticides are incorporated. Bat richness species was significantly related to the number of vegetation strata, height, and cover of trees. We suggest that coffee plantations could act as corridors, facilitating connection among different elements of the landscape in the Sierra Madre de Chiapas for some frugivorous and nectarivorous bats. [Copyright &y& Elsevier]

Abstract: Using the abundance and distribution of small mammals at 26 sites in an Atlantic forest landscape, we investigated how species abundance and alpha and beta diversity are affected by fragment size and the presence of corridors. To account for the variability in forest structure among fragments, we described and minimized the influence of foliage density and stratification on small mammal data. Sites were distributed among three categories of fragment size and in continuous forest. For small and medium-sized categories, we considered isolated fragments and fragments connected by corridors to larger remnants. Small mammal abundance and alpha and beta diversity were regressed against site scores from the first axis of a Principal Component Analysis on forest structure variables. Residuals were used in analyses of variance to compare fragment size and connectivity categories. Forest structure influenced total abundance and abundance of some species individually, but not the diversity of small mammal communities. Total abundance and alpha diversity were lower in small and medium-sized fragments than in large fragments and continuous forest, and in isolated compared to connected fragments. Three species were less common, but none was more abundant in smaller fragments. At least one species was more abundant in connected compared to isolated fragments. Beta diversity showed an opposite relationship to fragment size and corridors, increasing in small and isolated fragments. Results highlight the importance of secondary forest for the conservation of tropical fauna, the hyper-dynamism of small isolated fragments and the potential of corridors to buffer habitat fragmentation effects in tropical landscapes. [Copyright &y& Elsevier]

• Soil microbial diversity decreased along a natural aridity gradient. • Bacteria changed their proportion to adapted to environmental changes. • Fungi changed their rare taxa in response to environmental change. • Soil C:N, salinity and regional temperature regulate microbial community. • Soil C:N directly, and SPEI indirectly influence soil microbial diversity. Environmental aridity is increasing in several regions around the globe due to climate change. However, little is known about microbial diversity and community responses to aridity along grassland-to-desert gradients. We investigated soil bacterial and fungal diversity and composition, and associated environmental factors along an aridity gradient across grassland (G), desert-grassland (DG) and desert (D) in Inner Mongolia, Northern China. The results indicate that soil microbial diversity decreased significantly from G and DG to D. Bacteria were mostly dominated by the universal phyla Proteobacteria, Actinobacteria, Bacteroidetes and Acidobacteria. Fungal communities were dominated only by Ascomycota. Most bacterial species (58.7–69.1%) were found in all habitats with significant differences among the three vegetation types, while most soil fungal species occupied small geographic areas. Soil bacterial communities adapted to environmental changes through changes in proportions of their taxa, while fungi changed their rare taxa in response to the differences in local environments. Canonical correspondence analysis (CCA) indicated that soil C:N, salinity and regional temperature were the most important factors regulating microbial community composition. Structural equation models (SEM) revealed that C:N was the most important factor directly influencing soil microbial diversity, and SPEI was the most important factor indirectly influencing soil microbial diversity in the Mongolian desert-grassland ecosystem. Our results provide evidence that soil bacterial and fungal communities respond differently to the changes in the biotic and abiotic factors, reflecting different adaptive strategies for coping with climate change in desert grassland ecosystems. [ABSTRACT FROM AUTHOR]

• North African steppes are considered among the most threatened terrestrial biomes worldwide. • Grazing exclusion is an effective management practice for vegetation recovery and habitat restoration. • Implementing grazing exclusion during prolonged drought increases overall alpha-diversity. • Grazing exclusion increases abundance-based β-diversity at landscape scale. • The responses of plant functional groups to grazing exclusion were identity-dependent. Grazing exclusion has been proved to be an effective approach for naturally restoring degraded rangelands. Still, the effect of this management practice on plant community composition and structure is ambiguous, especially under prolonged and repeated drought events. Here, we investigated the responses of community composition (i.e. incidence-based) and structure (i.e. abundance-based) to short-term sheep grazing exclusion under severe drought episode in the arid steppes of Alfa-grass (Stipa tenacissima L.) with a long evolutionary history of grazing. Individual species responses were tested based on species occurrence and abundance in either grazed or grazing-excluded steppes. Besides, indicator species analysis was used to identify species indicative of grazing-excluded steppes. Likewise, incidence-based and abundance-based α -diversity, β -diversity and functional groups' diversities were quantified using Hill Numbers and compared between the two steppe managements types. Under severe drought conditions, sheep grazing exclusion allowed the apparition of a large number of increasers, colonizers, and native indicator plant species. It also improved the size of regional species pool and increased overall incidence-based and abundance-based α -diversity. Moreover, grazing exclusion decreased the abundance-based β -diversity at local scale but increased it at landscape scale. The incidence-based β -diversity significantly decreased at the landscape scale. Grazing exclusion enabled a significant spatial structuration of abundance-based β -diversity components by maintaining high balanced variation in species abundance at large spatial scale and greater abundance-gradient at fine-scale. Our results suggest that the implementation of short-term grazing exclusion in arid steppes would be the appropriate management practice for vegetation and habitat during prolonged droughts since it permits the recovery of native plant species and affects positively the size of the regional species pool, the overall incidence- and abundance-based α-diversity as well as the abundance-based β -diversity (chiefly at landscape scale). [ABSTRACT FROM AUTHOR]