Significant Differences In Diversity Research Articles

Comparative Analysis of the Gut Microbial Communities of the Eurasian Kestrel (Falco tinnunculus) at Different Developmental Stages.

The gut microflora play a very important role in the life of animals. Although an increasing number of studies have investigated the gut microbiota of birds in recent years, there is a lack of research work on the gut microbiota of wild birds, especially carnivorous raptors, which are thought to be pathogen vectors. There are also a lack of studies focused on the dynamics of the gut microbiota during development in raptors. In this study, 16S rRNA gene amplicon high-throughput sequencing was used to analyze the gut microbiota community composition of a medium-sized raptor, the Eurasian Kestrel (Falco tinnunculus), and to reveal stage-specific signatures in the gut microbiota of nestlings during the pre-fledging period. Moreover, differences in the gut microbiota between adults and nestlings in the same habitat were explored. The results indicated that the Eurasian Kestrel hosts a diverse assemblage of gut microbiota. Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes were the primary phyla shared within the guts of adults and chicks. However, adults harbored higher abundances of Proteobacteria while nestlings exhibited higher abundances of Firmicutes and Actinobacteria, and consequently the majority of dominant genera observed in chicks differed from those in adults. Although no significant differences in diversity were observed across the age groups during nestling ontogeny, chicks from all growth stages harbored richer and more diverse bacterial communities than adults. In contrast, the differences in gut microbial communities between adults and younger nestlings were more pronounced. The gut microbes of the nestlings in the last growth stage were converged with those of the adults. This study provides basic reference data for investigations of the gut microbiota community structure of wild birds and deepens our understanding of the dynamics of the gut microflora during raptor development.

Conservation Paleobiology as a Tool to Define Reference Conditions in Naturally Stressed Transitional Settings: Micropaleontological Insights from the Holocene of the Po Coastal Plain (Italy)

The key role of paralic environments as providers of ecosystem services, associated with their increasingly threatened state, led to the definition of international water management policies aimed to improve ecological quality status (EcoQs). Restoration actions rely on the definition of reference conditions, which is a particularly challenging task in naturally stressed transitional environments. In the present work, we apply the diversity index Exp(H’bc) on benthic foraminifer assemblages from two anthropogenically unimpacted transitional to coastal Holocene sediment successions of the Po coastal plain, in order to assess past EcoQs (PaleoEcoQs). Ostracod ecological groups provided detailed insights on naturally stressful paleoenvironmental conditions. We show that “poor” to “moderate” PaleoEcoQs are recorded by biological indicators at reference conditions under fluctuations of chemical-physical parameters and organic matter enrichment. We emphasize the importance of a site-specific paleobiological approach, as significant differences in diversity occur even on a short spatial scale. This study illustrates that early to mid-Holocene sediment successions resulted to be appropriate for conservation paleobiological purposes, providing a high-resolution paleoecological record under the influence of the Holocene sea-level rise in analogy with the present-day global change.

The Effect of Probiotics Supplementation on Gut Microbiota After Helicobacter pylori Eradication: A Multicenter Randomized Controlled Trial.

IntroductionHelicobacter pylori eradication therapy may lead to the perturbation of gut microbiota. We aim to investigate the impact of probiotics on eradication rate and gut microbiota during eradication therapy.MethodsA total of 162 patients receiving bismuth quadruple therapy were enrolled and randomly assigned to groups given probiotics (n = 83) or placebo (n = 79) for 4 weeks. Fecal samples were collected before treatment and 2, 4, 6, and 8 weeks after eradication therapy. Gut microbiota was analyzed by 16S rRNA high-throughput sequencing.ResultsThe eradication rates in the placebo and probiotics group were 82.43% and 87.01%, respectively (P > 0.05). Compared with baseline, alpha and beta diversity was significantly altered 2 weeks after eradication in both groups, which was restored at week 8. There were no significant differences in diversity between the two groups. H. pylori eradication therapy resulted in enrichment of some detrimental bacteria taxa such as Shigella, Klebsiella, and Streptococcus, while probiotics supplementation could rapidly restore these taxa levels after eradication and increase the taxa of Bacillus and Lactobacillales. Functional analysis revealed that lipopolysaccharide biosynthesis and polymyxin resistance pathways were significantly enriched after eradication, while probiotics supplementation mainly enriched the cofactors and vitamins metabolism pathways. Increased relative abundances of Roseburia and Dialister were associated with the positive eradication outcome.ConclusionsProbiotics supplementation might help to construct a beneficial profile of gut microbiota after eradication therapy. Specific bacteria taxa are associated with H. pylori eradication outcome. These findings may be of value in rational use of probiotics during H. pylori eradication.Trial RegistrationChinese Clinical Trial Registry, ChiCTR1900022116.Electronic supplementary materialThe online version of this article (10.1007/s40121-020-00372-9) contains supplementary material, which is available to authorized users.

Cross‐sectional comparisons of gut microbiome and short‐chain fatty acid levels among children with varied weight classifications

Limited studies associate changes in microbiota composition and metabolites among children and adolescents with obesity. Decreases in compositional diversity, increases in the proportion of Firmicutes and Bacteroidetes (F/B ratio) and increases in short-chain fatty acids (SCFAs) have been proposed as contributing factors in the pathophysiology of obesity. The aim of the current study was to characterize the faecal microbiota composition, diversity, F/B ratio and SCFA levels in different weight categories (lean, overweight, obesity classes 1-3) of children ages 5 to 12 years. We collected and processed 83 samples from different weight categories (27.7% lean, 11% overweight, 15%, 17% and 17% of obesity classes 1, 2, and 3, respectively). Microbiota content was determined by sequencing the V4 region of the 16S rRNA gene, and SCFA content was analyzed. Microbiota compositions showed no significant differences in diversity or F/B ratios between weight categories. However, a relative abundance of Proteobacteria and lack of Verrucomicrobia were demonstrated when comparing severe obesity to the leaner groups. Faecal butyrate, propionate and isopentanoate concentrations increased progressively with weight category demonstrating significance in the class 3 obesity group. Our results show that severe childhood obesity in our study population was associated with changes in gut microbiome composition correlated to previously reported cardiometabolic disease states in obesity. Increased SCFA levels correlate with obesity-related microbiome metabolic function without a reduction in diversity characterized at a phyla level. Further characterization of these specimens at a species level and longitudinal studies are needed to elucidate these relationships.

TMOD-19. INDIVIDUAL SPECIFIC HUMAN GUT MICROBE COMMUNITIES INFLUENCE RESPONSE TO IMMUNOTHERAPY IN A HUMANIZED MICROBIOME MOUSE MODEL OF GLIOMA

Abstract Although immunotherapy works well in glioblastoma (GBM) pre-clinical mouse models, the therapy has not demonstrated efficacy in GBM patients. Since recent studies have linked the gut microbial composition to the success with immunotherapy for other cancers, we utilized a novel humanized microbiome (HuM) model in order to study the response to immunotherapy in a pre-clinical mouse model of GBM. We used five healthy human donors for fecal transplantation of gnotobiotic mice since it is now recognized that microbe strain level differences render individual humans with a unique microbial community composition. After the transplanted microbiomes stabilized, the mice were bred to generate 5 independent humanized mouse lines (humanized microbiome HuM1-HuM5). Analysis of shotgun metagenomic sequencing data from fecal samples revealed a unique microbiome composition with significant differences in diversity and microbial composition among HuM1-HuM5 lines. We next analyzed the growth of intracranial glioma cells in the HuM lines. All HuM mouse lines were susceptible to GBM transplantation, and exhibited similar median survival ranging from 19-26 days. Interestingly, we found that HuM lines responded differently to the immune checkpoint inhibitor anti-PD-1. Specifically, we demonstrate that HuM1, HuM4, and HuM5 mice are non-responders to anti-PD-1 resulting in the death of the mice from the intracranial tumors, while HuM2 and HuM3 mice are responsive to anti-PD-1 and displayed significantly increased survival compared to isotype controls. Bray-Curtis cluster analysis of the 5 HuM gut microbial communities revealed that HuM2 and HuM3 were closely related. Detailed taxonomic comparison analysis at the top 5 across all HuM mouse lines revealed that Bacteroides cellulosilyticus was commonly found between HuM2 and HuM3 with high abundances. The results of our study establish the utility of humanized microbiome mice as avatars to delineate features of the host interaction with gut microbe communities needed for effective immunotherapy against GBM.

Investigating the cow skin and teat canal microbiomes of the bovine udder using different sampling and sequencing approaches

There is a need for standardized, efficient, and practical sampling methods to support large population-based studies of the internal and external epithelial microbiomes of the bovine udder. The primary objective of this study was to evaluate different sampling devices for the isolation of microbial DNA originating from the internal and external teat epithelium. Secondary objectives were to survey and compare the microbial diversity of external and teat canal epithelial microbiomes using amplicon and shotgun metagenomic sequencing approaches. To address these objectives, we enrolled a convenience sample of 24 Holstein dairy cows and collected samples from the external epithelium at the base of udder, the external teat barrel epithelium, the external teat apex epithelium, and the teat canal epithelium. Extracted DNA was quantified and subjected to PCR amplification of the V4 hypervariable region of the 16S rRNA gene and sequenced on the Illumina MiSeq platform (Illumina Inc., San Diego, CA). A subset of samples was subjected to a shallow shotgun metagenomic assay on the Illumina HiSeq platform. For samples collected from the external teat epithelium, we found that gauze squares consistently yielded more DNA than swabs, and Simpson's reciprocal index of diversity was higher for gauze than for swabs. The teat canal epithelial samples exhibited significantly lower diversity than the external sampling locations, but there were no significant differences in diversity between teat apex, teat barrel, and base of the udder samples. There were, however, differences in the microbial distribution and abundances of specific bacteria across external epithelial surfaces. The proportion of shotgun sequence reads classified as Bos taurus was highly variable between sampling locations, ranging from 0.33% in teat apex samples to 99.91% in teat canal samples. These results indicate that gauze squares should be considered for studying the microbiome of the external epithelium of the bovine udder, particularly if DNA yield must be maximized. Further, the relative proportion of host to non-host DNA present in samples collected from the internal and external teat epithelium should be considered when designing studies that utilize shotgun metagenomic sequencing.

Pinewood Nematode Alters the Endophytic and Rhizospheric Microbial Communities of Pinus massoniana.

Pinewood nematode, Bursaphelenchus xylophilus, is one of the greatest threats to pine trees and is spreading all over the world. During the nematode's pathogenesis, plant microorganisms play important roles. However, many microbial communities, such as that in Pinus massoniana, a major host of B. xylophilus that is widely distributed in China, are not well studied, especially the fungal communities. Here, the endophytic and rhizospheric bacterial and fungal communities associated with healthy and B. xylophilus-infected P. massoniana were analyzed. The results showed that 7639 bacterial and 3108 fungal OTUs were annotated from samples of P. massoniana, the rhizosphere, and B. xylophilus. There were significant diversity differences of endophytic microbes between healthy and infected P. massoniana. The abundances of endophytic bacteria Paenibacillus, unidentified_Burkholderiaceae, Serratia, Erwinia, and Pseudoxanthomonas and fungi Penicillifer, Zygoascus, Kirschsteiniothelia, Cyberlindnera, and Sporothrix in infected pines were greater than those in healthy pines, suggesting an association of particular microbial abundances with the pathogenesis of B. xylophilus in pines. Meanwhile, the abundances of microbes of unidentified_Burkholderiaceae, Saitozyma, and Pestalotiopsis were greater and Acidothermus and Trichoderma were lower in the rhizosphere under infected pines than those under healthy pines and the differences might be caused by B. xylophilus-induced weakening of the health of pines. Our study explored the endophytic and rhizospheric microbial community changes potentially caused by B. xylophilus infection of pines.

Regeneração natural em remanescentes de Floresta Ombrófila Mista sob diferentes manejos do estrato herbáceo

Visando contribuir para o melhor entendimento da regeneração da Floresta Ombrófila Mista (FOM), apresenta-se resultado de pesquisa que avaliou o impacto de dois tipos de manejo do estrato herbáceo como pastagem (tradicional e melhorada com sobressemeadura) na regeneração natural do componente arbóreo em remanescentes de FOM no Norte de Santa Catarina. Nestes locais, tradicionalmente, ocorre a extração da erva-mate associada a criação bovina leiteira, sistema regionalmente denominado de caíva. No geral, evidenciou-se que, independente do manejo adotado, a regeneração natural das espécies arbóreas típicas de FOM é um processo ativo, presente e contínuo nas caívas avaliadas. Evidenciou-se significativa diferença na diversidade e densidade total de indivíduos do componente de regeneração, sendo esta mais expressiva nas caívas sobressemeadas. A alta incidência de rebrotas e reduzida presença de indícios de indivíduos com dano por pastejo sugerem que as roçadas frequentes, mais do que o pisoteio e pastejo animal, são processos atrelados ao manejo das caívas que determinam importante impacto negativo sobre o componente regenerativo. Embora as caívas estudadas tenham apresentado níveis satisfatórios de regeneração, há necessidade da adoção de medidas que minimizem as pressões negativas atuantes no sistema.

Microbiota composition in bilateral healthy breast tissue and breast tumors.

Previous reports suggest that a complex microbiome exists within the female human breast that might contribute to breast cancer etiology. The purpose of this pilot study was to assess the variation in microbiota composition by breast side (left versus right) within individual women and compare the microbiota of normal and breast tumor tissue between women. We aimed to determine whether microbiota composition differs between these groups and whether certain bacterial taxa may be associated with breast tumors. Bilateral normal breast tissue samples (n = 36) were collected from ten women who received routine mammoplasty procedures. Archived breast tumor samples (n = 10) were obtained from a biorepository. DNA was extracted, amplified, and sequenced. Microbiota data were analyzed using QIIME and RStudio. The most abundant phyla in both tumor and normal tissues were Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria. There were statistically significant differences in the relative abundance of various bacterial taxa between groups. Alpha diversity (Simpson's index) was significantly higher in normal compared to tumor samples (0.968 vs. 0.957, p = 0.022). Based on unweighted UniFrac measures, breast tumor samples clustered distinctly from normal samples (R2 = 0.130; p = 0.01). Microbiota composition in normal samples clustered within women (R2 = 0.394; p = 0.01) and by breast side (left or right) within a woman (R2 = 0.189; p = 0.03). Significant differences in diversity between tumor and normal tissue and in composition between women and between breasts of the same woman were identified. These results warrant further research to investigate the relationship between microbiota and breast cancer.

Fish Assemblage Structure Comparison between Freshwater and Estuarine Habitats in the Lower Nakdong River, South Korea

Variabilities of biological communities in lower reaches of urban river systems are highly influenced by artificial constructions, alterations of flow regimes and episodic weather events. Impacts of estuary weirs on fish assemblages are particularly distinct because the weirs are disturbed in linking between freshwater and estuarine fish communities, and migration successes for regional fish fauna. This study conducted fish sampling at the lower reaches of the Nakdong River to assess spatio-temporal variations in fish assemblages, and effects of estuary weir on structuring fish assemblage between freshwater and estuary habitats. In total, 20,386 specimens comprising 78 species and 41 families were collected. The numerical dominant fish species were Tachysurus nitidus (48.8% in total abundance), Hemibarbus labeo (10.7%) and Chanodichthys erythropterus (3.6%) in the freshwater region, and Engraulis japonicus (10.0%), Nuchequula nuchalis (7.7%) and Clupea pallasii (5.2%) in the estuarine site. The fish sampled were primarily small species or the juveniles of larger species at the estuary region, while all life stages of fishes were observed at the freshwater habitats. The diversity patterns of fish assemblages varied greatly according to study site and season, with higher trends at estuarine sites during the warm-rainy season. No significant difference in diversity between freshwater and estuarine sites during the cold-dry season were found. Multivariate analyses of fish assemblage showed spatial and seasonal differences of assemblage structures. Higher effects of between-site variability but not within seasonal variability at each site were observed. Variations in assemblage structures were due to different contributions of dominant species in each habitat. Common freshwater species characterized the fish assemblage in the freshwater region, while marine juveniles were significantly associated with the estuarine habitat. The results from the ecological guild analyses showed distinct ecological roles for freshwater and marine species, and overlapping roles for fish sampled at the fishways. The lower reaches of the Nakdong River are an important ecosystem for both freshwater and marine juveniles. Nakdong River estuarine residents and migrant fishes, however, have been negatively affected by the construction of the weir (gravity dam), due to the obstruction to migration from and to freshwater habitats. Conservation and management policies aimed at minimizing anthropogenic influences on estuary ecosystems should focus on evaluating ecological functions of estuary weirs.

DNA mtCOI Barcodes for Maritime Biosecurity: A Proof of Concept in French Polynesia Ports

DNA barcodes have been proposed for diverse applications as markers for species identification. One application is not fully explored yet is their use for assessing the species biodiversity and presence of invasive alien species in maritime biosecurity. The phylogeographical signals of mtCOI gene have been sometimes used for inferring the number of introduction hits and the origin of biological invasions. Here we employed mtCOI barcodes of mollusks and acorn barnacles (N=751) from ports of the Windward Island of French Polynesia to infer the effect of port size, maritime traffic and degree of openness in the risk of biological invasions. With 17.2% of non-indigenous species recorded here, significant differences in diversity were found among docks, and between long-time docked ships and their closest piers. A higher proportion of non-indigenous species (NIS) was found from sheltered compared to open ports, regardless their size and traffic. Less frequent wave washing, lower effect of currents and partial isolation in sheltered ports could explain the difference. The results suggest that port biota surveys should focus first on ports sheltered from open sea and emphasize the value of mtCOI barcodes for early detection of potential invasive species, for prioritizing surveillance efforts.

Can be the environmental and biotic factors responsible for macroinvertebrate communities’ alterations in Portuguese alpine ponds?

Alpine ponds are shallow waterbodies formed in alpine zones characterized by usual pristine conditions, however subject to harsh conditions that enable the emergence of unique communities with high conservational value. Therefore, it is important to gather information about these ecosystems and understand the changes in the biota. This work aimed to use Portugal’s alpine ponds as a case of study in assessed the macroinvertebrates communities in the Mediterranean ecozone. To fulfill this goal, we aimed to understand the alterations on macroinvertebrates community and how are they modulated by environmental variables. Five alpine ponds in Serra da Estrela (Portugal) were studied for one year. Macroinvertebrate communities and physical and chemical water parameters were determined in June/16, October/16, and April/17. Water chemistry values were similar to other studied lentic waterbodies in alpine zones in Europe, with slightly acidic water and low conductivity. Although accentuated macroinvertebrates differences between ponds, no significant differences in diversity were recorded, indeed the main differences recorded were influenced by ponds habitat types and environmental variables. Canonical Correspondence Analysis showed differences in the communities between ponds, namely the high influence of several physical and chemical parameters (conductivity, phosphate content, and pH) in the macroinvertebrates community composition. Indeed, Spearman’s correlation revealed significant interaction in diversity, abundance and richness of macroinvertebrates and several physical and chemical parameters (pH, dissolved oxygen and nitrates concentration).

Gut microbiota dysbiosis in preeclampsia patients in the second and third trimesters.

BackgroundPreeclampsia (PE) is a serious complication that affects maternal and perinatal outcomes. However, the mechanisms have not been fully explained. This study was designed to analyze longitudinal gut microbiota alterations in pregnant women with and without PE in the second (T2) and third trimesters (T3).MethodsIn this nested case-control study, which was conducted at Nanjing Maternity and Child Health Care Hospital, fecal samples from 25 PE patients (25 fecal samples obtained in T2 and 15 fecal samples obtained in T3) and 25 matched healthy controls (25 fecal samples obtained in T2 and 22 fecal samples obtained in T3) were collected, and the microbiota were analyzed using 16S rRNA gene sequencing. The diversity and composition of the microbiota of PE cases and controls were compared.ResultsNo significant differences in diversity were found between the PE and control groups (P > 0.05). In the control group, from T2 to T3, the relative abundances of Proteobacteria (median [Q1, Q3]: 2.25% [1.24%, 3.30%] vs. 0.64% [0.20%, 1.20%], Z = −3.880, P < 0.05), and Tenericutes (median [Q1, Q3]: 0.12% [0.03%, 3.10%] vs. 0.03% [0.02%, 0.17%], Z = −2.369, P < 0.05) decreased significantly. In the PE group, the relative abundance of Bacteroidetes in T2 was lower than in T3 (median [Q1, Q3]: 18.16% [12.99%, 30.46%] vs. 31.09% [19.89%, 46.06%], Z = −2.417, P < 0.05). In T2, the relative abundances of mircrobiota showed no significant differences between the PE group and the control group. However, in T3, the relative abundance of Firmicutes was significantly lower in the PE group than in the control group (mean ± standard deviation: 60.62% ± 15.17% vs. 75.57% ± 11.53%, t = −3.405, P < 0.05). The relative abundances of Bacteroidetes, Proteobacteria, and Enterobacteriaceae were significantly higher in the PE group than in the control group (median [Q1, Q3]: 31.09% [19.89%, 46.06%] vs. 18.24% [12.90%, 32.04%], Z = −2.537, P < 0.05; 1.52% [1.05%, 2.61%] vs. 0.64% [0.20%, 1.20%], Z = −3.310, P < 0.05; 0.75% [0.20%, 1.00%] vs. 0.01% [0.004%, 0.023%], Z = −4.152, P < 0.05). Linear discriminant analysis combined effect size measurements analysis showed that the relative abundances of the phylum Bacteroidetes, class Bacteroidia and order Bacteroidales were increased in the PE group, while those of the phylum Firmicutes, the class Clostridia, the order Clostridiales, and the genus unidentified Lachnospiraceae were decreased in the PE group; and these differences were identified as taxonomic biomarkers of PE in T3.ConclusionFrom T2 to T3, there was an obvious alteration in the gut microbiota. The gut microbiota of PE patients in T3 was significantly different from that of the control group.

Different impacts of moderate human land use on the plant biodiversity of the characteristic Pannonian habitat complexes

Habitat complexes exhibit varying vulnerability to human land use and thus have different impacts on biodiversity. In this study, we analyzed the effect of moderate land use on the plant species diversity in six characteristic Pannonian habitat complexes: forest steppe complex on sand, on dolomite, and on loess, as well as alkaline habitat complex, freshwater marsh complex, and zonal broadleaf colline forest. We chose two regions for each complex, and in each region, we selected a 2 × 2 km “natural” study site in a mostly protected area, and a moderately used “managed” site of the same size. We compared the alpha, beta, and gamma diversities of the total and the specialist species pools of the natural-managed site pairs by applying stratified random sampling and novel bootstrap statistics.The gamma diversity of the specialist species pool was found to be the most sensitive indicator of naturalness. It was higher in the natural sites of the loess and dolomite forest steppe and the freshwater marshland complexes, while there were no significant diversity differences in the other complexes. The diversity comparisons showed a consistent pattern: there were either no significant diversity differences in any of the natural-managed pairs, or there were significant differences in the gamma diversities of the specialist species pool in both the natural-managed pairs.We concluded that the same differences in naturalness may represent different sensitivities to human management as characterized by differences in diversity measures. Three habitat complexes, the loess and dolomite forest steppe and the freshwater marshland, require more focused nature protection efforts in order to preserve the habitat diversity, especially in maintaining the remnants of the natural woody patches and the most inundated habitats of the marshlands. In the case of the other studied complexes, moderate human land use can be harmonized by nature protection goals.

Composition, Predicted Functions and Co-occurrence Networks of Rhizobacterial Communities Impacting Flowering Desert Events in the Atacama Desert, Chile.

Flowering desert (FD) events consist of the rapid flowering of a wide variety of native plants in the Atacama Desert of Chile, which is categorized as the driest desert in the world. While ephemeral plants are an integral part of the desert ecosystem, there is little knowledge on plant-microbe interactions that occur during FD events. Consequently, the overall goals of this present study were to investigate changes in the composition and potential functions of rhizobacterial community of Cistanthe longiscapa (Montiaceae) during the 2014 and 2015 FD events and determine the composition, potential functions, and co-occurrence networks of rhizobacterial community associated with the root zone of C. longiscapa during pre- (PF) and full-flowering (FF) phenological stages. Results of this study showed that the Proteobacteria and Actinobacteria were the dominant taxa in rhizosphere soils during the three FD events (2014, 2015, and 2017) examined. In general, greater microbial richness and diversity were observed in rhizosphere soils during the 2015-, compared with the 2014-FD event. Similarly, predicted functional analyses indicated that a larger number of sequences were assigned to information processing (e.g., ion channel, transporters and ribosome) and metabolism (e.g., lipids, nitrogen, and sulfur) during 2015 compared with 2014. Despite the lack of significant differences in diversity among PF and FF stages, the combined analysis of rhizobacterial community data, along with data concerning rhizosphere soil properties, evidenced differences among both phenological stages and suggested that sodium is a relevant abiotic factor shaping the rhizosphere. In general, no significant differences in predicted functions (most of them assigned to chemoheterotrophy, magnesium metabolisms, and fermentation) were observed among PF and FF. Co-occurrence analysis revealed the complex rhizobacterial interactions that occur in C. longiscapa during FD, highlighting to Kouleothrixaceae family as keystone taxa. Taken together this study shows that the composition and function of rhizobacteria vary among and during FD events, where some bacterial groups and their activity may influence the growth and flowering of native plants, and therefore, the ecology and trophic webs in Atacama Desert.

Diversity of root-associated culturable fungi of Cephalanthera rubra (Orchidaceae) in relation to soil characteristics.

Cephalanthera rubra (L.) Rich., Red Helleborine, is a widespread orchid in Europe but known only from three very small populations in England. These populations are in decline with no natural seed setting for more than a decade. The species may become extinct in the UK soon unless viable strategies are in place for ex situ conservation, especially the use of symbiotic propagation. Because of the fragile nature of the populations in England mycorrhizal fungal diversity study is not feasible. Therefore, to understand the factors needed for healthy Red Helleborine populations, soil characteristics and diversity of culturable root-derived fungi of the populations from a small area in the Loire Valley in France were studied. The main objectives of the study were: (1) Which culturable mycorrhizal fungi associated with C. rubra roots and (2) To what extent is variation in fungal communities related to variation in soil characteristics? Here, we report a significant difference in diversity of culturable mycorrhizal and non-mycorrhizal fungi depending on soil pH and phosphorus content. Mycorrhizal associations were favoured by plants in locations with low soil nutrient availability and comparatively higher pH. Our study shows that mycorrhizal fungi, both ecto and endo, can be cultured from roots of plants at different maturity stages.

Meiofaunal diversity at a seamount in the pacific ocean: A comprehensive study using environmental DNA and RNA

In deep-sea environments, which have low densities of large benthic animals, meiofauna are a useful indicator of biodiversity. However, in low-latitudes and in low-productivity areas, meiofaunal density is low, but is higher than that of megafaunal or macrofaunal density. Therefore, it is difficult to collect a sufficient number of specimens for statistical analysis. In addition, because faunal classification has been based on conventional microscopic observations, the use of meiofauna to estimate biodiversity in deep-sea environments is time-consuming. However, metabarcoding analyses focused on environmental DNA (eDNA) or RNA (eRNA) have recently been used to examine deep-sea eukaryotic diversity and communities. Here, we examined meiofaunal assemblages using microscopic, eDNA-, and eRNA-based methods at Xufu Guyot (JA06 Seamount), off the southeastern coast of Minami-Torishima Island in the North Pacific Ocean. Microscopic analysis failed to detect a significant difference in diversity or community structure between the seamount terrace and base. This was likely because of the low abundance of meiofauna, which was caused by the low surface productivity at the study area. However, eDNA/eRNA-based metabarcoding analyses revealed spatial variations in diversity and community structures within a single seamount. Therefore, metabarcoding analysis might be useful to elucidate meiofaunal assemblages in areas with low productivity and low faunal density.

Bioassessment of Mandakini River with the help of aquatic macroinvertebrates in the vicinity of Kedarnath Wildlife Sanctuary

Increasing advancement in development activities in the Indian Himalayan region in tandem with changing climate is influencing the ecological patterns of rivers. Thus, the present study investigates the effect of various degrees of anthropogenic stresses and possible implication of thermal dynamics of river water on the macroinvertebrate community in the Mandakini River, which flows in the vicinity of Kedarnath Wildlife Sanctuary of Chamoli district, Uttarakhand. The main objective was to study the community structure of macroinvertebrates in the Mandakini River and to calculate the effect of anthropogenic stresses on the macroinvertebrate community, particularly on Ephemeroptera, Plecoptera, and Trichoptera. The study was carried out in 10 spatially located sampling stations, and the frequency of sampling was divided into pre- and post-monsoon season (May and November 2017). Based on the degree of anthropogenic stresses, sampling locations were divided into least (Sonprayag), medium (Ukhimath), and high disturbed (Rudraprayag) sites. A total of 3257 individuals belonging to 7 orders and 21 families were found in both the sampling season. Diptera and Trichoptera were dominant orders in both the seasons, whereas Baetidae (Ephemeroptera), Hydropsychidae, Leptoceridae (Trichoptera) and Chironomidae (Diptera) were dominant families. Shannon diversity index varies from 2.048 to 2.25 in the least disturbed site (Sonprayag), 0.186–2.446 in medium disturbance (Ukhimath), and 1.362–2.271 in the highly disturbed site (Rudraprayag) in both the sampling season. Quantification of the EPT index shows a negative trend with an increase in anthropogenic stress, and it was least in Rudraprayag as compared to the other two sites. Result of one-way ANOVA shows a significant difference in diversity between pre- and post-monsoon season (p < 0.05). Analyzing the research gaps, it is recommended to have long-term ecological monitoring of high altitude and glacier-fed rivers and streams to obtain robust information regarding the dynamics of the riverine ecosystem in Garhwal Himalayas.

Microbiota Dysbiosis in Fungal Rhinosinusitis.

Fungal rhinosinusitis is a unique phenotype of chronic rhinosinusitis with unique clinical and histological characteristics. The role of bacterial microbiota in various phenotypes chronic rhinosinusitis is not thoroughly understood. Therefore, we conducted 16s rRNA amplification sequencing to determine differences in bacterial communities between phenotypes (fungal vs. non- fungal) and anatomical sites (middle meatus vs. nasopharynx). Endoscope-guided swabs were used to collect samples from the middle meatus and nasopharynx of seven consecutive patients with fungal and 18 consecutive patients with non-fungal rhinosinusitis. DNA was extracted and investigated through 16S rRNA amplification. Among samples from the middle meatus, Shannon diversity was significantly lower in those from the fungal rhinosinusitis group (p = 0.029). However, no significant differences in diversity were noted between nasopharynx samples (p = 0.85). Fungal rhinosinusitis samples exhibited a distinct distribution of taxon relative abundance, which involved not only the absence of rhinosinusitis-associated commensal Corynebacterium and Fusobacterium in the middle meatus but also a significant increase in Haemophilus prevalence and abundance. This is the first study to compare bacterial communities in fungal and non-fungal rhinosinusitis samples. Our findings demonstrated that bacterial community dysbiosis was more apparent in fungal rhinosinusitis samples and was limited to the middle meatus.

Effects of Mercury (Hg) on Soil Nematodes: A Microcosm Approach.

Mercury (Hg), one of the most toxic heavy metals, is commonly used in the gold extraction process in small-scale mining operations in many countries. Our previous field work on the impact of mining on soil nematode assemblages in a small-scale mining area in Sibutad, the Philippines, revealed no significant negative effects despite sometimes strongly elevated Hg concentrations. Using a microcosm approach, we now applied similar Hg concentrations as commonly found in these field sites (2.5, 5, and 10mg/kg Hg) and determined their impact on nematode assemblages from a different soil with different physicochemical soil attributes. Our results demonstrate (a) limited "bottling" effects (incubation effects) after a 45-day incubation period: a nematode abundance decrease of up to 37%, but absence of significant differences in diversity and nematode assemblage composition; (b) that total nematode abundance already decreased at Hg concentrations (2.5mg/kg), which did not yield significant impacts on other nematode assemblage descriptors, such as assemblage composition and different diversity indices; and (c) that the Hg concentrations found in the Sibutad field sites can be detrimental to soil nematode assemblages. The discrepancy between our microcosm and the field-based results is probably related to differences in physicochemical soil attributes (e.g., OM contents, soil pH), which suggests that nematode-based environmental assessments should be interpreted in a context-dependent manner.