University campuses as urban biodiversity refugia: butterfly diversity and community turnover in Northern Mindanao, Philippines

Soil samples were collected at the fallow period, flowering stage, and fruiting stage of tomato under tomato-melon (TM) and tomato-bean (TB) systems. Illumina MiSeq high-throughput pyrosequencing was performed to analyze the differences in AM fungal community between the two rotation systems. We further analyzed the key factors driving the changes in AM fungal diversity and community composition. Results showed that rotation with legume significantly altered the α-diversity of AM fungi. Shannon diversity and Pielou evenness of AM fungi under the TB system were 24.9% and 24.0% lower than that under TM system, respectively. Compared to the fallow period, richness, Shannon diversity, and phylogenetic diversity of AM fungi at the tomato flowering and fruiting stages decreased significantly by 55.6%-67.5%, 49.6%-51.5%, and 21.4%-23.7%, respectively. Rotation with legume (the TB system) promoted the relative abundance of Glomus in all the three sampling times, but reduced the relative abundance of Paraglomus and Archaeospora at the flowering and fruiting stages. Claroideoglomus was more abundant in soils under the TM system than that under the TB system at the fallow period, but the pattern was the opposite at the flowering stage. Ambispora, Diversispora, and Scutellospora were detected only in soil under the TB system. Results of permutational multivariate analysis of variance (PERMANOVA) and non-metric multidimensional scaling (NMDS) analysis showed that both rotation system and growing stage significantly affected the structure of AM fungal community. Soil moisture, pH, and Olsen-P were the predominant factors controlling the variations in the diversity and composition of AM fungal community. Results of structural equation modeling (SEM) further indicated that rotation system and growing stage affected the variations in AM fungal diversity and community structure indirectly via changing soil pH.

Maintaining species turnover across habitats is essential for biodiversity conservation. Thus, identifying drivers of community variation is important for conservation strategies. Here, we examine spider community variation along a Mediterranean climatic gradient in Greece, characterised by a mosaic of vegetation. We quantified spider community composition in 22 sites including three different habitat types (grassland, shrubland, oak forest) along a temperature gradient. Community composition was assessed at the family and species (Gnaphosidae and allied families) level. We partitioned beta diversity into two additive components, turnover/balanced abundance variation and nestedness/abundance gradient. Permutational multivariate analysis of variance was used to assess the effects of habitat type, temperature, humidity and elevation on beta diversity. Results showed that different habitat types harboured distinct spider communities at both taxonomical levels. Turnover and balanced abundance variation of families and species were the largest beta diversity components. Turnover and balanced abundance variation of species but not families were significantly affected by temperature differences and the rate of compositional change was similar in grasslands and forests. We conclude that maintaining habitat heterogeneity in the area will conserve spider diversity and that future rising temperatures may potentially lead to species replacement and to changes in the chorological spectrum of the communities. Applying beta diversity partitioning at small spatial scales can offer valuable insights into climate change effects and sustain the development of appropriate conservation actions, especially in cases where temporal or coarser-scale distributional data are lacking. Given their sensitivity, ground spiders are good indicators of climate change effects on biodiversity.

Flies (Diptera) are the dominant animal in the North yet are underrepresented in ecological studies. Our study aimed to examine the diversity patterns of the poorly documented acalyptrate flies across the Canadian North. Our main objective was to determine large- and small-scale drivers of species richness, abundance and community composition of acalyptrate fly assemblages. We collected flies at 12 Canadian sites in three ecoclimatic zones (Northern Boreal, Sub-Arctic and High Arctic), from two habitats (wet and mesic). We tested the effect of climatic variables and habitat on species richness and abundance using a generalized linear mixed-effects model, and on community composition using permutational multivariate analysis of variance. Species turnover between sites and ecoclimatic zones was examined by testing for multivariate homogeneity of group dispersions and visualised using non-metric multidimensional scaling. We identified 3631 acalyptrate flies, belonging to 333 species. Diversity measures and community composition were associated with seasonal and limiting temperature variables, consistent with the latitudinal diversity gradient seen in other animal groups. However, habitat only explained a small portion of the variation in our data, and only for observed species richness and species composition. Turnover patterns showed slight, statistically non-significant variation across zones. The High Arctic ecoclimatic zone was as spatially heterogenous in composition as the Northern Boreal and Sub-Arctic ecoclimatic zones but hinted at complex interplays between geographical and glacial legacies. Our results contradict the historical view of Arctic arthropod diversity as simple and uniform, and may serve as a baseline for future biodiversity monitoring.

Positive effects of low grazing intensity on East African bee assemblages mediated by increases in floral resources

Anthropogenic expansion extensively covers Earth's cultivable surface, increasing pressure on ecosystems and leading to significant biodiversity loss and widespread pollution, particularly impacting freshwater systems. Diffuse agricultural pollution, stemming from agrochemical runoff into river channels, represents a critical threat to aquatic biota. Mayflies (Ephemeroptera), with their sensitive obligately subaquatic immature stages, are excellent bioindicators of water quality. This study investigated how mayfly communities in Northwestern Argentina, a region dominated by sugarcane and citrus cultivation, respond to such diffuse pollution. Our primary objective was to determine if mayfly community characteristics (total abundance, species richness, and assemblage composition) exhibit changes downstream of cultivated areas compared to upstream sections. We collected 277 D-net samples across five rivers, at both upstream and downstream sites relative to cultivation, each two months (over nine visits) during 2009-2010. The impact of agriculture at downstream sites on mayfly abundance and richness is not uniform across all rivers, with significant reductions observed in some rivers, but not others. Non-metric multidimensional scaling and permutational multivariate analysis of variance confirmed significant effects of site, river, and their interaction on community composition. Notably, the difference in composition between upstream and downstream sites was significant. SIMPER analysis identified Baetodes as the primary contributor to upstream-downstream dissimilarities, being more abundant upstream. Indicator species analysis highlighted Haplohyphes baritu, Lachlania sp., and Nanomis galera as indicators of specific upstream conditions, while no species were exclusive indicators of downstream sites, suggesting downstream communities may be a depauperate subset. These findings underscore the context-dependent impact of diffuse agricultural pollution on mayfly communities and their utility as bioindicators.

The identification of factors promoting biodiversity and, more specifically, the causes that contribute to beta diversity is a central and growing issue in ecology. In this study, we used long-term data (1999–2007, including a pronounced drawdown in 2000) to assess the beta diversity partitioning of aquatic macrophyte assemblages in five arms of the Itaipu reservoir. We partitioned beta diversity (βsor) into two components: nestedness (βnes) and species turnover (βsim). To check whether environmental variables (electrical conductivity, water transparency, and fetch) were correlated with the components of beta diversity, we used a permutational multivariate analysis of variance. Over the study period (1999–2007), we observed high values of beta diversity and prevalence of spatial turnover of the species. They were correlated with all environmental factors studied, which demonstrated significant interactions. Dendritic-shaped arms, high shore development, local physical and chemical conditions of the water, and biotic interactions could be determining factors for the prevalence of spatial turnover of aquatic macrophyte assemblages. The drawdown promoted an enormous quantity of dead macrophyte biomass, specifically submerged species that preferentially colonized shallow margins of the reservoir. On the other hand, large open areas were available for colonization of ruderal species and seed bank germination. This dynamic led to an increase of beta diversity and turnover values in the year of the drawdown compared to the 1999 and 2001. This pattern remained until the end of the study, characterizing the aquatic macrophytes of the Itaipu reservoir as an assemblage with high beta diversity and prevalence of species turnover over nestedness, among and within arms.

The multi-faceted impacts of the Anthropocene are increasingly modifying natural ecosystems and threatening biodiversity. Protected spaces in and adjacent to urban landscapes may be critical in protecting species in human-modified systems. Can small, protected spaces act as reservoirs for biodiversity across dynamic spatial and temporal gradients of human impact? To address this question, we identified small mammal remains from modern raptor pellets and Holocene archaeological sites along a human modification gradient in the San Francisco Bay Area, CA. We assessed small mammal alpha and beta diversity for both modern and Holocene sites. We tested for significant differences between sites and time bins using permutational multivariate analysis of variance (PERMANOVA) and visualized these differences using non-metric multidimensional scaling (NMDS). We found that alpha diversity decreased with increasing human modification in Anthropocene sites, with no corresponding change between Holocene sites. Additionally, the alpha diversity of modern sites with moderate/high levels of human modification was significantly lower than that of protected modern sites and all Holocene sites, driven by the dominance of human-commensal and disturbance-tolerant species. On the other hand, the small mammal communities from a small, protected area (Jasper Ridge Biological Preserve) retained Holocene levels of alpha diversity. Jasper Ridge has also changed less over time in terms of overall community composition than more modified sites. Despite this, both PERMANOVA and NMDS show that Holocene and Anthropocene communities are significantly distinct regardless of collection site and level of anthropogenic modification. Our results suggest that even relatively small, protected spaces within an urbanized matrix conserve native faunal communities, highlighting their important role in urban conservation.

The inland lakes of Isle Royale National Park have remained relatively isolated from human impact, providing an opportunity to explore how fish diversity responds to climate change with minimal confounding effects. We analyzed fish assemblages of 23 lakes sampled in the 1920s, 1990s, and 2020s to 1) assess shifts in multiple diversity metrics, 2) identify lakes and species experiencing the most change, 3) explore environmental factors driving community structure, and 4) determine changes in length and abundance of common species. We used species-area curves, Permutational Multivariate Analysis of Variance (PERMANOVA), and multivariate dispersion tests to quantify differences in diversity between surveys, temporal beta diversity indices to identify lakes and species changing most, and Non-metric Multidimensional Scaling (NMDS) to examine lake factors influencing composition. We assessed changes in length and abundance using linear mixed-effect models and Wilcoxon signed-rank tests. Mean richness and species-area curves did not significantly differ between survey dates, although both declined slightly. PERMANOVA and dispersion tests indicated overall community composition and spatial variability remained mostly stable, but larger lakes became more dominated by cool-water species. Species gains and losses were associated with isostatic rebound rate, where lakes with fast and slow rebound rates tended to gain and lose species, respectively, compared to prior studies. Sculpin and stickleback species were most commonly lost, while blackchin shiner and pumpkinseed were most commonly gained. Larger lakes hosted more diverse communities, and lakes with higher elevation lacked northern pike and yellow perch. Abundance increased for northern pike but declined for yellow perch and walleye, while average size increased for northern pike and walleye. Overall, these results suggest the inland lake fish communities of Isle Royale have not homogenized over time, but assemblages have gained cool-water and lost several cold-water species. More consistent surveys will be required to determine which species will persist in the future and whether undetected species have been extirpated.

The Darjeeling district of West Bengal, India, is an ideal home to many taxa, like any other part of the Great Himalayas. The floristic survey of the Darjeeling district provides an overview of the region's biodiversity within the Eastern Himalayan hotspot. The present study documented diverse plant taxa from the Darjeeling Himalaya by preparing herbarium specimens using standard methods, identifying them taxonomically and assessing their threat status using the IUCN Red List database. Using floristic inventories analysed through diversity indices (Shannon, Simpson, Margalef), similarity measures (Jaccard, Sørensen), non-metric multidimensional scaling (NMDS) ordination and permutational multivariate analysis of variance (PERMANOVA), quantified the spatial patterns of plant diversity across the study area. This study showed that Orchidaceae, Rosaceae, Lamiaceae, Fabaceae and Acanthaceae are the dominant plant families in the area and recorded 11 plant species that are either endemic or regionally restricted. The study revealed high alpha diversity (species richness 40–109; H′ = 3.69–4.69) and strong beta diversity driven mainly by species turnover (Jaccard dissimilarity 0.28–0.94), with altitude and associated temperature gradients significantly structuring community composition (PERMANOVA R² = 0.316, p = 0.001), whereas precipitation had no significant effect. The conservation status shows that almost 76 % of the plant species are in the "Not Evaluated" (NE) category, followed by "Least Concern" (LC; 19 %), "Endangered" (EN; 1.2 %) and "Critically Endangered" (CR; 1%). The floristic exploration data on species richness and diversity of the flora provide valuable baseline data for future studies.

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Studies on the natural regeneration of tree species communities are important for providing information on forest development capacity. This research aimed to evaluate the floristic-structural variations of the tree regenerative component along a topographic gradient in an ecotonal area between a Mixed Ombrophilous Forest and a Deciduous Seasonal Forest of Santa Catarina, Brazil. 30 sampling units of which all regenerating tree species individuals have been identified were allocated in the forest fragment. The sampling units were then distributed along a topographic gradient into lower, intermediate and upper sectors. Abundance, richness, Shannon's diversity index (H') and Pielou's evenness index (J) have been determined for both the whole community as for each sector. The community floristic-structural organization was verified by the means of the non-metric multidimensional scaling (NMDS), the indicator species analysis and the permutational multivariate analysis of variance (PERMANOVA). Abundance differences among sectors were analyzed through the Kruskal-Wallis test with post hoc multiple nonparametric test while richness differences were verified through rarefaction. Regenerating individuals density in the upper sector [129 (21.300 ind.ha-1)] was lower than both in the lower [401 (63.800 ind.ha-1)] and intermediary [241 (36.300 ind.ha-1)] sectors. There was variation in the floristic-structural composition (p < 0.001) among topographic positions; the lower sector was the most distinct one and showed the highest number of indicator species.

Previous studies have identified alterations in the faecal microbiota of horses with colic; however, further work is needed to interpret these findings. To compare the faecal microbiota of horses presenting for colic at hospital admission, day 1 and day 3/discharge and with different colic duration and lesion locations. Prospective observational clinical study. Faecal samples were collected from 17 colic cases at hospital admission, on day 1 and on day 3 post-admission or at the time of hospital discharge if prior to 72hours. Faecal samples were extracted for genomic DNA, PCR-amplified, sequenced and analysed using QIIME. Species richness and Shannon diversity (alpha diversity) were estimated. The extent of the relationship between bacterial communities (beta diversity) was quantified using pairwise UniFrac distances, visualised using principal coordinate analysis (PCoA) and statistically analysed using permutational multivariate analysis of variance (PERMANOVA). The relative abundance of bacterial populations at the different time points and in different types of colic was compared using ANCOM. There was a decrease in species richness from admission to day 3/hospital discharge (P<.05), and a lower species richness (P=.005) and Shannon diversity (P=.02) in horses with colic ≥60h compared to <60h. Based on PCoA and PERMANOVA, there was a significant difference in bacterial community composition for horses with different colic duration (P=.001) and lesion location (P=.006). Several differences in bacterial phyla and genera were observed at different time points and with different types of colic. Relatively low numbers and a diverse population of horses. The microbiota change from hospital admission to day 3/discharge in horses with colic and horses with colic ≥60h and large colon lesions have a distinct bacterial population compared to horses with colic <60h and small intestinal lesions.

Nitrate-dependent iron oxidation (NDFO) is a novel mechanism for microbial bioremediation of metal and metalloid contaminants. During NDFO, microbes catalyze a redox reaction wherein nitrate is reduced to nitrite and nitrogen gas while Fe(II) is oxidized to solid Fe(III) hydroxide minerals. Metalloid contaminants such as selenium and arsenic have a propensity for adsorption to iron minerals produced during NDFO; some contaminants may also be concurrently bioreduced. A number of bacterial isolates have been shown to be capable of NDFO (e.g., Kappler et al. (2005), Kiskira et al. (2017)), but little work has been done to date characterizing mixed microbial communities performing NDFO. Some autotrophic communities have been characterized, with high relative abundances for strains of Gallionellaceae in both a freshwater sediment enrichment culture and an activated sludge culture (Blöthe and Roden 2009, Tian et al. 2020). In mixotrophic activated sludge cultures, the concentration of Fe(II) amendment was found to significantly impact microbial community composition; these cultures were fed with methanol in addition to Fe(II), and the dominant community members were Methyloversatilis and other methylotrophic strains (Liu et al. 2018). The work presented here examines microbial communities performing NDFO in the context of remediation, and in particular how differences between NDFO and heterotrophic communities may influence remediation effectiveness. This research characterizes and compares microbial communities performing NDFO versus heterotrophic denitrification during removal of selenium and nickel from mining wastewater. Sediment and influent water from a subsurface bioreactor treating mining wastewater were used to construct batch bioreactors, which were amended with selenium and nickel as well as either Fe(II) or methanol to investigate contaminant removal and microbial community composition in NDFO versus heterotrophic microbial communities. Both Fe(II) and methanol reactors removed total aqueous selenium to below the quantification limit, but Fe(II) reactors removed it more rapidly, likely due to adsorption of selenite. For nickel, removal to below the detection limit was achieved with methanol amendment, while Fe(II) amendment resulted in 42-95% removal. This was likely due to precipitation of nickel sulfide during sulfate reduction in methanol-amended reactors. DNA from the batch bioreactors will be sequenced and the results analyzed for differences among communities. Permutational multivariate analysis of variance and non-metric multidimensional scaling will be used to determine significant correlations of community composition with experimental variables, selenium and nickel removal, and NDFO (Roberts 2023, Kruskal 1964). Indicator species analyses (De Cáceres et al. 2010) will be applied to identify taxa found significantly more often (i.e., at a higher relative abundance) in one group of microbial communities than in any other group. The indicator species analysis may reveal whether there are groups of denitrifiers that predominate in NDFO conditions vs. groups that predominate during heterotrophic denitrification. The results of these microbial community analyses, in combination with the geochemical analyses, will improve our understanding of microbial communities performing NDFO in remediation environments.

ABSTRACTBackground: Increased soil phosphorus (P) caused by agricultural intensification has been associated with decreased plant species richness (SR) in central Europe. How plant communities and soil P gradients are related in unimproved open habitats remains unclear.Aims: The aim of this article was to characterise the relationship between soil chemical parameters and plant species composition and richness in unimproved open habitats.Methods: The influence of soil chemical parameters (pH, P, K, Mg) on species composition was assessed, using data from 40 heathland and 54 grassland plots, by non-metric multidimensional scaling and permutational multivariate analysis of variance. The relationship between soil chemical parameters and SR was tested by linear mixed effects models.Results: A direct relationship between heathland community composition and pH was observed, explaining 10% of variation in species composition, while P, Mg and pH together explained 17% of variation in grassland composition. In heathlands, SR increased with increasing pH, whereas in grasslands, SR decreased with increasing soil P.Conclusions: Soil chemical parameters were substantially related to plant community composition and richness. In an area spared from a century of agricultural intensification, reduced pH appeared to constrain SR in heathlands, while even slight P increases (<10 mg kg−1) depressed plant SR in semi-natural grasslands.

Understanding the biodiversity of aquatic communities and the underlying mechanisms that shape biodiversity patterns and community dynamics is crucial for the effective conservation and management of freshwater ecosystems. However, traditional survey methods often fail to comprehensively capture species diversity, particularly for low-abundance taxa. Moreover, studies integrating both metazoan and fish communities at fine spatial scales remain limited. To address these gaps, we employed a multi-marker eDNA metabarcoding approach, targeting both the 12S and 18S rRNA gene regions, to comprehensively investigate the composition of metazoan and fish communities in the Yujiang River. A total of 12 metazoan orders were detected, encompassing 15 families, 21 genera, and 19 species. For the fish community, 32 species were identified, belonging to 25 genera, 10 families, and 7 orders. Among these, Adula falcatoides and Coptodon zillii were identified as the most prevalent and abundant metazoan and fish species, respectively. Notably, the most prevalent fish species, C. zillii and Oreochromis niloticus, are both recognized as invasive species. The Bray–Curtis distance of metazoa (average: 0.464) was significantly lower than that of fish communities (average: 0.797), suggesting higher community heterogeneity among fish assemblages. Beta-diversity decomposition indicated that variations in the metazoan and fish communities were predominantly driven by species replacement (turnover) (65.4% and 70.9% for metazoa and fish, respectively) rather than nestedness. Mantel tests further revealed that species turnover in metazoan communities was most strongly influenced by water temperature, while fish community turnover was primarily affected by water transparency, likely reflecting the physiological sensitivity of metazoans to thermal gradients and the dependence of fish on visual cues for foraging and habitat selection. In addition, a co-occurrence network of metazoan and fish species was constructed, highlighting potential predator-prey interactions between native species and Corbicula fluminea, which emerged as a potential keystone species. Overall, this study demonstrates the utility of multi-marker eDNA metabarcoding in characterizing aquatic community structures and provides new insights into the spatial dynamics and species interactions within river ecosystems.