Biodiversity monitoring in remote marine environments: Advancing environmental DNA/RNA sampling workflows.

Recent advances in environmental DNA‐based biodiversity assessment and conservation

ANALYZING OR EXPLAINING BETA DIVERSITY? COMMENT.

BackgroundEquine pastern dermatitis (EPD) is a multifactorial syndrome, with prolonged exposure to moisture assumed to be a predisposing or primary factor.Hypothesis/ObjectivesTo examine the course of EPD lesion severity, changes in bacterial skin microbiota, and the influence of meteorological factors.AnimalsProspective, longitudinal cohort study over a one‐year period, with six Franches‐Montagnes stallions, four affected by EPD and two unaffected, that were kept under the same conditions.Methods and materialsPasterns were scored for lesion severity and sampled once a month for 12 consecutive months. Lesion severity, the skin microbiota and meteorological factors were examined for associations.ResultsEPD lesions tended to worsen in autumn and at the beginning of spring. The relationship between lesion severity and the meteorological factor precipitation was not clearly evident; high scores were preceded by both low or high rates of precipitation. Microbiota in affected pasterns appeared to have experienced a reduction in alpha diversity. Beta diversity analyses demonstrated that bacterial community structures were altered in affected versus unaffected pasterns, and that alterations were more pronounced with higher EPD scores (P = 0.005). Meteorological factors also had considerable influences on the bacterial composition, whereby these influences appeared to be more marked in the affected pasterns (P = 0.001, F = 3.19) than in unaffected ones (P = 0.005, F = 1.83).Conclusions and clinical relevanceOur study provides preliminary observations of the relationships between lesion severity, meteorological factors and cutaneous bacteria. The population was too small to draw firm conclusions, and further studies on environmental factors and the involvement of bacteria in this multifactorial disease are needed.

AimTo evaluate the ability of precipitation‐based environmental DNA (eDNA) sample collection and mitochondrial 12S metabarcoding sequencing to reconstruct well‐studied fish communities in lakes and rivers. Specific objectives were to 1) determine correlations between eDNA species detections and known community composition based on conventional field sampling, 2) compare efficiency of eDNA to detect fish biodiversity among systems with variable morphologies and trophic states, and 3) determine if species habitat preferences predict eDNA detection.LocationUpper Great Lakes Region, North America.MethodsFish community composition was estimated for seven lakes and two Mississippi River navigation pools using sequence data from the mitochondrial 12S gene amplified from 10 to 50 water samples per waterbody collected in 50‐mL centrifuge tubes at a single time point. Environmental DNA (eDNA) was concentrated without filtration by centrifuging samples to reduce per‐sample handling time. Taxonomic detections from eDNA were compared to established community monitoring databases containing up to 40 years of sampling and a detailed habitat/substrate preference matrix to identify patterns of bias.ResultsMitochondrial 12S gene metabarcoding detected 15%–47% of the known species at each waterbody and 30%–76% of known genera. Non‐metric multidimensional scaling (NMDS) assessment of the community structure indicated that eDNA‐detected communities grouped in a similar pattern as known communities. Discriminant analysis of principal components indicated that there was a high degree of overlap in habitat/substrate preference of eDNA‐detected and eDNA‐undetected species suggesting limited habitat bias for eDNA sampling.Main conclusionsLarge numbers of small volume samples sequenced at the mitochondrial 12S gene can describe the coarse community structure of freshwater systems. However, additional conventional sampling and environmental DNA sampling may be necessary for a complete diversity census.

Hulun Lake, a UNESCO Biosphere Reserve, faces mounting threats from extreme climate events and anthropogenic pressures, highlighting the need for robust biodiversity monitoring. Environmental DNA (eDNA) has emerged as a promising tool for aquatic biomonitoring, yet different bioinformatic pipelines-such as Amplicon Sequence Variant (ASV) and Operational Taxonomic Unit (OTU) clustering-may yield divergent results. This study compares ASV and OTU clustering approaches in eDNA metabarcoding alongside traditional capture-based surveys to assess fish diversity in Hulun Lake. Across all methods, we identified 43 taxa (40 species), including the critically endangered Acheilognathus hypselonotus and vulnerable Choi's spiny loach (Cobitis choii). While eDNA methods detected 2~3 times more species than in nets (13 species), strong methodological correlations (p < 0.001) were observed between net frequencies and eDNA-derived relative abundances (based on both ASV and OTU datasets using 4th-root and log transformations). Clustering analysis of capture-based data revealed four distinct ecological zones: the areas near tourist facilities, Wuerxun River inflow region, Wulan Nuoer Lake (connected via the Wuerxun River), and the Lake Centre. Significant spatial variation (p < 0.05) between these four zones was found in eDNA datasets, whereas nets captured more heterogeneous patterns, consistent with previous studies. Community structures were shaped by both generalists (e.g., Cyprinus carpio, Hemiculter bleekeri) and habitat specialists such as Amur catfish (Silurus asotus). The Lake Centre hosted a unique assemblage, likely due to reduced human disturbance. Overall, both eDNA clustering methods outperformed capture-based survey in detecting species richness and offered semi-quantitative insights. However, discrepancies between ASV and OTU approaches were evident in resolving fine-scale community differences. We recommend an integrated monitoring strategy that combines the sensitivity of eDNA with the abundance resolution of net captured to inform spatially targeted conservation and habitat protection in this vulnerable ecosystem.

AimClimate change and anthropogenic environmental deterioration strongly affect aquatic microbial communities. Although microbes have irreplaceable roles in various ecosystems, the spatial variation in microbial communities has received less attention in comparison to macro‐organisms. Studies aiming to disentangle the effects of local environmental, catchment and climatic variables on microbial communities are also rare. Here, we disentangled the effects of local, catchment, spatial and climatic variables on boreal stream diatom and bacterial communities.LocationWestern FinlandMethodsWe sampled 21 boreal river basins comprising 105 study sites spanning 520 km in north‐south direction and 330 km in east‐west direction in western Finland. We used principal coordinates of neighbour matrix analysis (PCNM), redundancy analyses (RDA), variation partitioning, boosted regression trees (BRT) and regression analyses to examine variation in community composition and species richness.ResultsWater chemistry and physical variables had significant effects on the community composition of both microbial groups. Catchment level variables explained a slightly larger amount of variation in diatom community composition than local level variables. Agriculture was the most significant determinant of variation in diatom community composition among catchment level variables and was also related with variation in the richness of both groups. Of spatial and climatic variables, growing degree days (GDD) and spatial variables were the most significant drivers determining diatom community composition. GDD was also positively associated with the richness of diatoms and bacteria. Unique effects of spatial and climate variables accounted for the largest amount of variation in the community composition of both diatoms and bacteria.Main conclusionsOur results highlight that aquatic microbial communities can exhibit biogeographical variation at regional scales due to the joint influence of local, catchment and climatic variables, and possibly because of dispersal limitation. Catchment properties, especially agriculture, can be used as a proxy for the effects of landscape alteration on aquatic microbial communities.

Sulawesi and its satellite archipelagos lie within the Wallacea region and Coral Triangle biodiversity “hotspots”. Environmental DNA (eDNA) metabarcoding can help detect easily missed or challenging to identify groups such as blennies (Blenniiformes). A pilot eDNA study within the recently established Banggai MPA aimed to provide fine-scale data. Seawater samples were collected at four sites (3 replicates/site) around Banggai Island. DNA extraction (Bionesia, Bali), metabarcoding (MiFish 12S rRNA primers) and sequence library preparation (Barber Lab, University of California Los Angeles), Nextseq High-throughput sequencing, and Anacapa Toolkit analysis produced 254,847 teleost reads aggregated into amplicon sequence variants (ASVs). At 60%, 90% and 100% Bayesian confidence levels, respectively, 1612, 1610 and 1573 reads were assigned to Blenniiformes, while 15 of 20, 12 of 20 and 11 of 18 ASVs were assigned to species level. Blenniiformes ASVs comprised two families: Blenniidae (genera Atrosalarias, Cirripectes, Ecsenius, Exallias, Meiacanthus, Omobranchus, Salarias) and Tripterygiidae (genus Enneapterygius). Assigned genera overlapped with 1998 visual survey data. Phylogenetic analysis (MEGA 11) incorporated NCBI GenBank accessions (BLASTn tool). Blenniiformes community composition differed between sites. This study contributes baseline biodiversity data for Blenniiformes in the Banggai MPA; however, unassigned ASVs and phylogenetic analyses highlight the gaps in 12S rRNA reference databases.

Predictors of fine-scale spatial variation in soil mite and microbe community composition differ between biotic groups and habitats

Rhizospheric bacterial communities in plants contribute to drought resilience by promoting plant-soil interactions, yet their biodiversity and ecological impacts are not fully characterized. In cowpeas, these interactions may be crucial in enhancing tolerance to drought conditions. In this study, cowpea plants were subjected to drought treatment, the soil attached to the roots was collected, environmental DNA (e-DNA) was extracted, and the bacterial communities were identified as amplicon sequence variants (ASVs) by metagenomics analysis of the 16S rRNA gene. Microbial communities under drought and control conditions were analyzed using taxonomy and diversity metrics. The sequencing results revealed 5,571 ASVs, and taxonomic analysis identified 1,752 bacterial species. Alpha and beta diversity analyses showed less conserved microbial community structures and compositions among the samples isolated from the rhizosphere under drought conditions compared to untreated samples, implying the enhancement effect of drought on species' biodiversity and richness. The differential accumulation analysis of the bacterial community identified 75 species that accumulated significantly (P ≤ 0.05) in response to drought, including 13 species exclusively present, seven absent, and 46 forming a high-abundance cluster within the hierarchical heatmap. These species were also grouped into specific clades in the phylogenetic tree, suggesting common genetic ancestry and potentially shared traits associated with drought tolerance. The differentially accumulated bacterial list included previously characterized species from drought and saline habitats. These findings suggest that drought stress significantly alters the composition and abundance of epiphytic bacterial communities, potentially impacting the rhizosphere's ecological balance and interactions with cowpeas. The results highlight microbial adaptations that enhance plant resilience through improved stress mitigation, providing meaningful understandings for advancing sustainable agriculture and developing microbial-based strategies to boost crop productivity in drought-prone regions.

BackgroundLaying hens with access to outdoor ranges are exposed to additional environmental factors and microorganisms, including potential pathogens. Differences in composition of the cloacal microbial community between indoor- and outdoor-housed layers may serve as an indicator for exposure to the outdoor environment, including its pathogens, and may yield insights into factors affecting the chickens’ microbiota community dynamics. However, little is known about the influence of outdoor housing on microbiota community composition in commercial layer flocks. We performed a cross-sectional field study to evaluate differences in the cloacal microbiota of indoor- vs outdoor-layers across farms.Eight layer flocks (four indoor, four outdoor) from five commercial poultry farms were sampled. Indoor and outdoor flocks with the same rearing flock of origin, age, and breed were selected. In each flock, cloacal swabs were taken from ten layers, and microbiota were analysed with 16S rRNA gene amplicon sequencing.ResultsHousing type (indoor vs outdoor), rearing farm, farm and poultry house within the farm all significantly contributed to bacterial community composition. Poultry house explained most of the variation (20.9%), while housing type only explained 0.2% of the variation in community composition. Bacterial diversity was higher in indoor-layers than in outdoor-layers, and indoor-layers also had more variation in their bacterial community composition. No phyla or genera were found to be differentially abundant between indoor and outdoor poultry houses. One amplicon sequence variant was exclusively present in outdoor-layers across all outdoor poultry houses, and was identified as Dietzia maris.ConclusionsThis study shows that exposure to an outdoor environment is responsible for a relatively small proportion of the community variation in the microbiota of layers. The poultry house, farm, and rearing flock play a much greater role in determining the cloacal microbiota composition of adult laying hens. Overall, measuring differences in cloacal microbiota of layers as an indicator for the level of exposure to potential pathogens and biosecurity seems of limited practical use. To gain more insight into environmental drivers of the gut microbiota, future research should aim at investigating community composition of commercial layer flocks over time.

Rumen microbes serve a vital role in feed utilization of ruminant animals, suggesting the potential of rumen microbiota to influence inter-animal variation in nutrient utilization. There is limited knowledge surrounding the influence of the rumen bacterial community in animals selected based on feed efficiency. The objective of this study was to examine the differences in the rumen bacterial community in replacement Holstein heifers with divergent genomically enhanced breeding values for residual feed intake (RFIg). Genomic breeding values for RFIg were based on RFI phenotypes of 6,563 growing Holstein heifers from STgenetics ongoing EcoFeed research program. Holstein heifers (n = 55; initial BW = 351 ± 64 kg) with low RFIg (n = 29) or high RFIg (n = 26) were selected from a contemporary group of 453 heifers (RFIg = -0.023 ± 0.211 kg/d). These heifers were assigned to 1 of 2 pens, equipped with electronic feedbunks (GrowSafe Systems) and a GreenFeed gaseous-exchange measurement system (C-Lock). Individual DMI was collected for 84-d and BW measured weekly to determine phenotypic RFI. On d-70 of the study, a rumen sample was collected from each animal via esophageal tubing and bacterial community composition determined through 16S rRNA gene sequencing of the V4 region. A total of 523 amplicon sequence variants (ASVs) were observed among the 55 samples, with the average reads per sample of 54,107 ± 42,688 across samples. To examine the rumen bacterial composition, permutational multivariate analysis of variance (PERMANOVA) utilizing the weighted and unweighted Unifrac distance matrix was used. Utilizing the weighted Unifrac no differences (P = 0.513) were observed in the bacterial composition of the rumen content between heifers with divergent RFIg; however, utilizing the unweighted Unifrac differences (P = 0.031) were identified in the bacterial composition between heifers with divergent RFIg. Based on alpha diversity metrics, observed ASVs displayed greater (P = 0.015) bacterial richness in high- compared with low-RFIg heifers; however, there was no difference (P = 0.500) in the Shannon diversity index between heifers with divergent RFIg. ASV level classification of the most differentially abundant (P &amp;lt; 0.05; log2-fold change &amp;gt; 1) ASVs demonstrated that three ASVs from the bacterial family Prevotellaceae, and one ASV from the bacterial family Ruminococcaceae was predominant in high- compared with low-RFIg heifers. Additionally, one ASV belonging to the family Prevotellaceae was predominant in low- heifers compared with their high-RFIg counterparts. Results from this study indicate greater enrichment of ruminal bacteria in high RFIg cattle, with ASVs from the Prevotellaceae and Ruminococcaceae families differing between heifers with divergent RFIg. Opportunities exist to further investigate the role of the rumen microbiome in selection of cattle based on genomic RFI, and to assess associations between specific bacterial ASVs and phenotypic feed efficiency traits in cattle.

Deforestation and forest degradation in Andean forests is influenced by natural and social environments including a wide elevation range and anthropogenic disturbance. Tree community composition is receiving attention as a key indicator of forest degradation. However, difference in factors affecting community composition at different elevation zones remains unclear. We aimed at elucidating factors (natural and human disturbances, and forest characteristics) that influence the variations in community composition in Andean forests. We conducted a ground-based survey setting 45 plots across a wide elevation range (ca. 600 to 3500 m a.s.l.) in Cusco region, Peru. Above ground biomass (AGB) decreased with increasing elevation. The generalized linear models for multivariate abundance data suggested that a factor affecting community composition was natural disturbance (erosion) at low elevation (&lt;1000 m), while human disturbance (infrastructure such as sheds and trails) at high elevation (≥2400 m). Within each of the different elevation zones, the AGB affected community composition only at mid elevation (1000–2400 m), whereas mean tree height showed a consistent effect on community composition across the three elevations. Our results suggest that the effects of human disturbance on community composition were more prominent at higher elevation. The results also suggest that mean tree height may have a potential to be a key measure for evaluating variations in community composition in Andean forests.

Spatial and environmental drivers of macrophyte diversity and community composition in temperate and tropical calcareous rivers

Algarte V.M., and Rodrigues L. 2013. How periphytic algae respond to short-term emersion in a subtropical floodplain in Brazil. Phycologia 52: 557–564. DOI: 10.2116/12-112.1Changes in hydrometric levels caused by dam operations can alter community structure in aquatic environments. We investigated the effects of a short-term emersion on a periphyton community in a lentic environment in a subtropical floodplain in Brazil. Our goals were to identify variations in periphyton community structure and composition during a period of 21 days subsequent to a short-term emersion and to identify taxa associated with periphyton after the emersion event. In situ, we simulated 15 hours of emersion of the periphyton community during the climax stage and investigated the effects of emersion on the structure and composition of this community over 21 days. Periphyton was removed by scrubbing randomly chosen glass slides from the support controls and the treatments. The structure and composition of the periphyton community showed variations soon after emersion, e.g. new taxa were recorded, the diatoms and oedogoniophyceans were lost; furthermore, the community did not return to its initial successional phase after the disturbance. Canonical ordination analysis showed a variation in community composition and structure throughout the successional period, and axis two indicated variation in the community soon after the emersion disturbance occurred in the control and treatment periphyton. Similarities between the control and treatment periphyton communities were lower soon after emersion and higher after the fifth day after emersion. Loosely attached species characterised the treatment periphyton after the disturbance. Recovery of the periphyton community may have been influenced by the reproduction of persistent species and by recruitment from the regional species pool. Short-term emersion affected the structure and composition of the periphyton community in the Upper Paraná floodplain; however, its rapid recovery to pre-disturbance conditions suggested that it is already adapted to the intensified variations that occur in this system because of dam operations.

Differences in habitat associations or responses to environmental stressors among broadly co-distributed species can result in local variation in community composition. As a result, ongoing environmental change may drive shifts in community composition, especially at range peripheries. In the present study, we describe regional variation in avian community composition at the southern extent of the boreal zone. Boreal bird communities are disproportionally influenced by ongoing climate change and contain several declining species. Here we observe the habitat associations for 13 boreal bird species, and assess the link between species' habitat associations and community composition. We conducted standardized point counts at 20 boreal forest sites in northeastern United States and Canada, and quantified the vegetation structure and composition as well as the climate at each site. We found large variation in the habitat associations among co-distributed boreal birds, both in terms of the specific variables important for each species and in the breadth of habitat types occupied. These findings suggest that species within this community will vary in their responses to environmental change, potentially resulting in changes to the boreal avian community.