Assessing Freshwater Microbiomes from Different Storage Sources in the Caribbean Using DNA Metabarcoding

Spatial patterns of macrobenthic alpha and beta diversity at different scales in Italian transitional waters (central Mediterranean)

ANALYZING OR EXPLAINING BETA DIVERSITY? COMMENT.

Species diversity is determined as Alpha or Beta level. Other levels of diversity come up to different scales of the Alpha and Beta diversity. Alpha diversity is calculated intra-medium, while Beta diversity is calculated inter-medium. Physiographic and edaphically factors affect species diversity significantly. For this reason, It is necessary that species diversity must be contacted with Physiographic and edaphically factors, which is an argument in ecology. When applied for species diversity expression instead of an ecosystem expression, a lot of alive groups such as plants, animals, insects, soil microorganism are mentioned. For this reason, to determine species diversity as qualitative and quantitative is an investigation combined by the disciplines such as botanic, entomology, zoology altogether. But Ecology intends to investigate relationships between this diversity dates and site factors. In this way, underlying areas in protection, areas having rich species diversity as potential, changes in species diversity with time and effects of different factors on species diversity in the similar environment can be determined. Keywords: Diversity index, Species diversity, Alpha-Beta-Gamma diversity

Pregnancy prompts a cascade of anatomical, metabolic, hormonal, and immunological adaptations important for foetal development, labour and birth(1). These multi–system adaptations interact with the maternal gut microbiome and may affect pregnancy and infancy outcomes(2). However, the nature and extent of changes to gut microbiome composition and diversity during pregnancy and the influence of dietary intake remains contentious. The ‘BABY1000’ pilot prospective birth cohort study based in Sydney, Australia(3) sought to explore associations between maternal diet, the maternal gut microbiome before and across pregnancy, and the infant gut microbiome. Primary aims were to (1) explore the composition and diversity of the gut microbiome of women at preconception, at 12-, 28- and 36-weeks’ gestation, and in infants at six weeks of age; and (2) determine how maternal and infant gut microbiomes are influenced by diet quality and fibre intake during pregnancy. Mothers (n = 146) and infants (n = 105), encompassing 86 mother–infant dyads were involved. RStudio (v 4.2.3) was used to perform microbiome composition and diversity analyses using 350 maternal and 102 infant stool samples. Maternal dietary quality was assessed at recruitment (preconception or 12 weeks’ gestation) and at 36 weeks’ gestation using the Australian Eating Survey (AES)(4). At the group level, maternal dietary quality was suboptimal and did not change significantly across pregnancy (mean scores of 37.5 ± 7.3 and 38.3 ± 6.7 out of 73 points at recruitment and late pregnancy, respectively; p > 0.05). Although differences in gut microbiome alpha (within–person) diversity between mothers and infants was highly significant (p < 0.0001), no differences in gut microbiome composition or diversity related to pregnancy status or gestational stage were observed. Maternal diet quality in pregnancy was also not significantly correlated with microbial beta (between–people) diversity in samples taken in late pregnancy (PERMANOVA: R2 = 0.039, p > 0.05). When fibre intake was separated into quartiles, there was a significant (p < 0.01) difference in alpha diversity between the lowest and highest quartiles of intake, though differences in beta diversity were not significant (PERMANOVA: R2 = 0.06, p > 0.05). Microbiota composition and diversity in infant samples was also not significantly affected by maternal dietary quality or fibre intake, but rather by birth mode and feeding type. Significantly different clustering of infant samples was clear between vaginal and caesarean births (PERMANOVA: R2 = 0.029, p = 0.005). Gut bacterial alpha diversity was significantly lower (p < 0.01) between infants receiving breastmilk compared to formula. As this area of research is still in its ‘infancy’, appropriately powered longitudinal studies are required to understand the processes that shape diet and microbiome interactions during the critical first 1,000 days of life and beyond.

Contrasting processes drive alpha and beta taxonomic, functional and phylogenetic diversity of orthopteran communities in grasslands

Los artrópodos del suelo son un componente importante de la biota del suelo por su diversidad de especies, función y como herramienta para evaluar el estado de conservación del hábitat. Este estudio evaluó el estado de conservación de tres sectores en un ecosistema de alta montaña (Socha, Tasco y Socotá en Boyacá, Colombia) por medio de la medición de la diversidad alfa y beta del ensamblaje de artrópodos epigeos con referencia hacia Acari y Collembola. Se instalaron trampas de caída siguiendo transectos en cada sector; se midió la diversidad alfa por medio del índice de Berger-Parker y el modelo gamma-binomial para obtener un parámetro α, que describe el ajuste del ensamblaje a una distribución de abundancias. Se estimó la diversidad de especies por medio de curvas de rarefacción-extrapolación basadas en la cobertura de abundancias y la diversidad beta se midió en sus componentes, reemplazamiento y diferencia de especies. La diversidad alfa no mostró diferencias estadísticas entre sectores, pero con la mayor riqueza de especies en el sector de Socotá. El parámetro α indicó que el sector Socotá es el mejor conservado; similar a lo obtenido con Acari y Collembola. El reemplazamiento o la diferencia de especies mostró cambios con respecto al sector o grupo taxonómico (Acari o Collembola), explicado por la estructura de la vegetación, erosión y distribución agregada de los artrópodos epigeos. La utilidad de los artrópodos epigeos para evaluar la calidad del hábitat y la partición de la diversidad beta en sus componentes fue analizada.

Riparian forests are known to be floristically diverse and influenced by multiscale phenomena, yet few studies have explicitly compared how these factors contribute to various aspects of riparian plant diversity. We analyzed woody riparian plant species and environmental data from four western Oregon watersheds distributed across a wide climate‐driven productivity gradient at three scales (40‐m2 sample plots [alpha diversity], 1‐ha plots, and species pools from 16 1‐ha plots in each watershed) to compare three hypotheses of control on species diversity: (1) local control, (2) direct climatic control, and (3) indirect climatic control. We used a process model (3‐PG) to model gross primary productivity (GPP) as a functional climate index across our study area. We performed multiple linear regression to determine the best predictors of alpha (sample‐plot scale) diversity, compositional change within riparian forests (beta diversity), and hectare‐scale diversity and used path analysis to explore hypothesized causal linkages between climate and other factors and species diversity. We also analyzed a companion data set of gap and forest environments from a subset of the same sites to determine the influence of disturbance on species diversity across the gradient.We found evidence for strong spatial patterning in woody plant richness consistent with indirect climatic control on woody plant richness. Climate (GPP) showed negative relationships with alpha diversity and hectare richness of trees, shrubs, and woody plant species and was the most commonly selected explanatory variable in regression analyses. GPP and Rubus spectabilis cover increased from the least to most productive climates while understory light and moisture heterogeneity across the riparian area decreased. These environmental changes coincided with declines in alpha, beta, and hectare‐scale diversity. Disturbance gaps yielded higher richness at most sites, but differences in species richness between gap and forest sample plots did not increase at high levels of GPP, as hypothesized.This study points toward an integrated conceptual model whereby regional and landscape scale controls such as climate and watershed position complement and interact with local controls (i.e., vegetation structure, environmental gradients) to jointly govern woody plant diversity in riparian forests.

Species diversity in a habitat is often termed alpha diversity. As it influences various community properties, many studies have investigated its drivers. For instance, intertidal macroalgal canopies limit understory thermal stress during low tides and thus often increase alpha diversity. More recently, beta diversity has also become of interest. Beta diversity measures the change in species composition across space and is another important attribute of communities because it influences their multifunctionality, productivity, and resilience. Using data from a field experiment done in Atlantic Canada, we tested the hypothesis that fucoid macroalgal canopies limit beta diversity in intertidal communities. This prediction stems from previous evidence that such canopies limit thermal variation across the substrate during low tides, an important consideration because spatial thermal changes influence spatial variability in species composition. To test our hypothesis, we compared two treatments (full canopy cover and canopy removal) created the year before on intertidal areas that were originally all fully covered by canopies. Separately for each treatment, we calculated beta diversity as the Bray-Curtis dissimilarity between nearby quadrats using species abundance data. Overall, fucoid macroalgal canopies significantly reduced beta diversity, showing that these foundation species can have opposing effects on alpha and beta diversity.

Simple SummaryThe selection of fish community survey methods based on their efficiency and reliability is critical for ecosystem conservation, protection and management. In this study, we used environmental DNA (eDNA) metabarcoding and traditional (gillnet) fishing to assess the diversity of fishes along a mangrove–seagrass–coral reef continuum of marine habitats in Hainan, China. Higher fish taxonomic diversity was identified using eDNA; however, gillnet fishing was better at identifying fish communities from different habitats along the sampled continuum. Results from both survey methods indicate that some fish species use multiple habitats along mangrove–seagrass–coral reef continuums. Therefore, the concurrent use of eDNA and gillnet survey methods provides a more comprehensive approach to understanding the heterogeneity of fish taxonomic and functional diversity along mangrove–seagrass–coral reef continuums.The effective and reliable monitoring of fish communities is important for the management and protection of marine ecosystems. Environmental DNA (eDNA) metabarcoding is a relatively new method that has been widely used in recent years, while traditional sampling via fish catching (i.e., gillnets) is one of the most common and reliable fish monitoring methods used to date. We compared the taxonomic and functional diversity of fish detected within a mangrove–seagrass–coral reef continuum using both survey methods. One liter seawater and gillnet samples were collected in August 2021 from mangrove forests, seagrass meadows and coral reef habitats (n = 3 each) in Hainan, China. Surveys using eDNA and gillnets identified 139 genera belonging to 66 families and 58 genera belonging to 42 families, respectively. Regardless of the survey method, fish detected in mangrove, seagrass and coral reef habitats were heterogeneous in their communities; however, the shared species between habitats suggest some degree of connectivity. There were no significant differences between habitats in terms of taxonomic and functional diversity, but a higher taxonomic diversity was detected using eDNA. Both methods were able to distinguish fish assemblages between different habitats; however, gillnet surveys performed better than eDNA surveys for distinguishing mangrove from seagrass assemblages. Therefore, the concurrent use of eDNA and gillnet survey methods provides a more comprehensive approach to understanding the heterogeneity of fish taxonomic and functional diversity along mangrove–seagrass–coral reef continuums.

Gut Microbiota Is Significantly Impacted by Feeding Mode and Associated With Growth Status in Exclusively Breastfed and Formula-Fed US Infants

The purpose of this study was to document gamma diversity of Chironomidae in Outer Mongolia by documenting alpha and beta diversity of chironomids from streams sites within Gorkhi Terelj National Park and in the surrounding area. Pupal exuviae of Chironomidae were collected from streams using standardized, semi-quantitative sampling methods so that patterns in community structure could be compared to patterns in the study sites. Gamma diversity for the twelve sites in this study was 98 species, including 26 new records for Mongolia; alpha diversity of Chironomidae ranged from 3 to 37 species. Beta diversity ranged from 0–0.44 and mean beta diversity was 0.17. Species diversity did not correlate to distance between sites. The Chao 1 species estimator estimated 126 species of Chironomidae from the streams in Gorkhi Terelj National Park. Ad hoc analysis comparing chironomid communities from Gorkhi Terelj National Park and Lake Hovsgol area stream and lake sites increased the estimated number of species to 144. Dominant species were used in a double dendrogram analysis which yielded three distinct communities of chironomids which corresponded to three clusters of study sites that differed by habitat type, water quality, and physical characteristics. This study produced data for use in conservation of streams in Gorkhi Terelj National Park.

Prior work has shown a positive scaling relationship between vertebrate body size, human height, and gut microbiome alpha diversity. This observation mirrors commonly observed species area relationships (SARs) in many other ecosystems. Here, we expand these observations to several large datasets, showing that this size-diversity scaling relationship is independent of relevant covariates, like diet, body mass index, age, sex, bowel movement frequency, antibiotic usage, and cardiometabolic health markers. Island biogeography theory (IBT), which predicts that larger islands tend to harbor greater species diversity through neutral demographic processes, provides a simple mechanism for positive SARs. Using a gut-adapted IBT model, we demonstrated that increasing the length of a flow-through ecosystem led to increased species diversity, closely matching our empirical observations. We delve into the possible clinical implications of these SARs in the American Gut cohort. Consistent with prior observations that lower alpha diversity is a risk factor for Clostridioides difficile infection (CDI), we found that individuals who reported a history of CDI were shorter than those who did not and that this relationship was mediated by alpha diversity. We observed that vegetable consumption had a much stronger association with CDI history, which was also partially mediated by alpha diversity. In summary, we find that the positive scaling observed between body size and gut alpha diversity can be plausibly explained by a gut-adapted IBT model, may be related to CDI risk, and vegetable intake appears to independently mitigate this risk, although additional work is needed to validate the potential disease risk implications.

Exploring trophic effects of spotted knapweed (Centaurea stoebe L.) on arthropod diversity using DNA metabarcoding

AimComponents of scale, such as grain, focus and extent, influence the spatial patterns of alpha and gamma diversity and the relationships between them. We explored these scale relations by testing whether the gamma diversity and alpha diversity along an elevation gradient were related independent of scale and whether the elevational patterns of herbaceous and woody species richness were dependent on scale.LocationLangtang National Park, Nepal.MethodsWe estimated alpha diversity (plot richness) for woody and herbaceous plant species along an alpine elevation gradient (3,900–5,000 m a.s.l.) in nested plots of 1 m2, 16 m2 and 100 m2 and gamma diversity (regional richness) from published sources. Generalized linear modelling was used to analyse alpha and gamma diversity and their correspondence at different grain sizes.ResultsElevational trends of gamma and alpha diversity were significantly correlated for both woody and herbaceous species at all grain sizes. The concordance increased with increasing grain size and area for gamma diversity estimation, particularly for the monotonously decreasing elevational gamma and alpha diversity patterns of woody species. The hump‐shaped patterns of elevational gamma and alpha diversity for herbaceous species were also significantly correlated, but the concordance between the alpha diversity of herbaceous species and local gamma diversity was stronger. Elevational patterns of alpha diversity were coarsely consistent across grain sizes, although the patterns became more pronounced at larger grain sizes.Main conclusionsThe correspondence of elevational gamma and alpha diversity was largely scale invariant, implying that elevational and possibly other geographical diversity patterns can reliably be studied at different spatial scales. Nonetheless, the alpha diversity pattern was the least pronounced at fine grain size, particularly for woody life‐forms. This finding suggests that for large‐scale patterns such as elevational gradients at regional or continental scales, coarse grain sizes and large areas for gamma estimation are more appropriate.

Context Acarina are commonly collected in macroinvertebrate surveys used to monitor freshwater ecosystems. However, they can be difficult to identify morphologically requiring considerable taxonomic skill for identification to finer taxonomic levels. Therefore, in biomonitoring they are identified to subclass despite high species diversity and varied environmental responses. DNA barcoding individuals and DNA metabarcoding of bulk samples enables species to be accurately and routinely identified. However, poor DNA barcode coverage of Australian aquatic mites has hampered their use in DNA studies. Aims Here, we aim to generate DNA barcodes for mites from Greater Melbourne, Australia. Key results For many specimens, we link DNA barcodes to genus-level morphological identifications using genetic analysis of DNA barcodes to understand biodiversity. We then test if new DNA barcodes can improve identification of mites in samples processed with DNA metabarcoding. We found Australian aquatic mites showed high diversity with many DNA barcodes represented by single specimens. Conclusions Increased mite DNA barcode library coverage improved their detection using DNA metabarcoding. Implications Given high species diversity, much effort will be required to improve DNA barcode coverage for aquatic mites in Australia and integrate barcodes with species level taxonomy, allowing Acarina to be better incorporated into DNA-based biological monitoring.