Unique Amplicon Sequence Variants Research Articles

Seminal plasma microbiomes, sperm parameters, and cryopreservation in a healthy fertile population.

Recent advances in microbiome research have revealed the presence of diverse microbial communities in human tissues previously thought to be sterile. The present study delves into the emerging field of seminal plasma microbiomics, examining the relationship between semen microbes and semen parameters and post-freezing tolerance. The study involved a cohort of healthy fertility males and microbial genome analysis using 16S rRNA to characterize the microbial diversity of seminal plasma. Microbial diversity analysis identified unique amplicon sequence variants (ASVs) and genera dominant in seminal plasma. Spearman's correlation coefficient was used to assess the relationship between flora and semen parameters. A paired t-test was used to compare the changes in microbiome expression in seminal plasma before and after cryo-resuscitation. The relevant results show that the top five phyla in terms of abundance of seminal plasma microbiome were Firmicutes, Bacteroidota, Proteobacteria, Actinobacteriota, and Campylobacterota. Spearman correlation analysis highlighted the association between specific microbial species and semen parameters, between Porphyromonas_asaccharolytica and sperm concentration. Microbial changed significantly after cryo-resuscitation, affecting taxonomic units such as Campylobacter and Muribaculaceae, and KEGG enrichment analyses, suggesting that metabolic pathways are associated with sperm freezing. Eubacterium_coprostanoligenes and Eptoniphilus_duerdenii exhibited a potential impact, while Orynebacterium_tuberculostearicum demonstrated a positive correlation with the recovery rate of progressive motile sperm. The semen of normal fertile individuals contains a microflora component that is closely related to semen quality, including the sperm's ability to withstand freezing.

Bacterial dynamics and biotic sources in the developing swimming crab embryos

The microbial community associated with aquatic animals begins to assemble from the embryonic stage and plays a vital role in their growth and survival. However, the microbial community of the swimming crab Portunus trituberculatus during its embryonic period has not yet been studied. In this study, we investigated the embryonic bacterial community (EBC) of this species across the developmental cycle to elucidate its longitudinal dynamics and biotic sources. The results showed that the diversity of the EBC decreased with host development. The composition of the EBC varied across embryonic development, with a high percent of persistent bacteria and the gradual replacement of γ-Proteobacteria (mainly Oceanospirillaceae and Colwelliaceae) by α-Proteobacteria (Rhodobacteraceae and Flavobacteriaceae) as the major signatures of the succession patterns. Moreover, the unique amplicon sequence variants (ASVs) exhibited the highest functional potentials at the cleavage stage, whereas the shared ASVs did so at the later stages. Furthermore, maternal tissue, mainly the ovary and abdominal setae, contributed the most to the EBC, while rearing water contributed minimally. Overall, our results reveal succession patterns and biotic sources of EBC during the developmental cycle, highlighting that the dominance of embryonic bacteria starts from the early stage of embryo and bacterial vertical transmission is of significance during embryonic development. We also suggest the necessity of microbial management from maternal crabs.

The diversity, composition and functions of soil bacterial communities surrounding Syowa Station, East Antarctica, under different intensities of human disturbances

Since the establishment of Syowa Station over six decades ago, the study on the terrestrial bacterial community surrounding the station has been notably lacking and inadequately documented. Using the latest sequencing technology, we revealed the soil bacterial composition from soil samples collected from the surrounding of the station. In doing so, we also assessed the effect of human disturbances brought upon by different activities in the proximity of the station, in contrast to those in less human interference and pristine areas. Our results show that human activities near the main station facilities, especially within the 100-m range, visibly changed the structure and functions of the soil microbial community. Areas with high levels of human disturbances displayed a decrease in both microbial diversity and richness, accompanied by a lower count of unique amplicon sequence variants (ASVs) compared to regions with intermediate and low human disturbances. Moreover, higher proportions of functions related to hydrocarbon degradation were also predicted from samples collected within this area. In contrast, soil microbial communities from intermediate and low human disturbances samples have higher proportions of bacterial groups and functions consistent with those in undisturbed natural habitats.

Microbial community and extracellular polymeric substance dynamics in arid–zone temporary pan ecosystems

Microbial extracellular polymeric substances (EPS) are an important component in sediment ecology. However, most research is highly skewed towards the northern hemisphere and in more permanent systems. This paper investigates EPS (i.e., carbohydrates and proteins) dynamics in arid Austral zone temporary pans sediments. Colorimetric methods and sequence–based metagenomics techniques were employed in a series of small temporary pan ecosystems characterised by alternating wet and dry hydroperiods. Microbial community patterns of distribution were evaluated between seasons (hot–wet and cool–dry) and across depths (and inferred inundation period) based on estimated elevation. Carbohydrates generally occurred in relatively higher proportions than proteins; the carbohydrate:protein ratio was 2.8:1 and 1.6:1 for the dry and wet season respectively, suggesting that EPS found in these systems was largely diatom produced. The wet– hydroperiods (Carbohydrate mean 102 μg g−1; Protein mean 65 μg g−1) supported more EPS production as compared to the dry– hydroperiods (Carbohydrate mean 73 μg g−1; Protein mean 26 μg g−1). A total of 15,042 Unique Amplicon Sequence Variants (ASVs) were allocated to 51 bacterial phyla and 1127 genera. The most abundant genera had commonality in high temperature tolerance, with Firmicutes, Actinobacteria and Proteobacteria in high abundances. Microbial communities were more distinct between seasons compared to within seasons which further suggested that the observed metagenome functions could be seasonally driven. This study's findings implied that there were high levels of denitrification by mostly nitric oxide reductase and nitrite reductase enzymes. EPS production was high in the hot–wet season as compared to relatively lower rates of nitrification in the cool–dry season by ammonia monooxygenases. Both EPS quantities and metagenome functions were highly associated with availability of water, with high rates being mainly associated with wet– hydroperiods compared to dry– hydroperiods. These data suggest that extended dry periods threaten microbially mediated processes in temporary wetlands, with implications to loss of biodiversity by desiccation.

Microeukaryotic communities diversity with a special emphasis on protozoa taxa in an integrated wastewater treatment system

This study developed an integrated wastewater treatment system that combines an upflow anaerobic sludge blanket (UASB), downflow hanging non-woven fabric (DHNW), and anaerobic baffled reactor (ABR) to explore the effect of treatment stages on the diversity of microeukaryotic communities. This study aimed to bridge the knowledge gap regarding the influence of integrated system stages on microeukaryotic community diversity. Through 18S rRNA amplicon sequencing, we identified unique microeukaryotic communities across different stages, with the aerobic phase hosting 35.77% of unique amplicon sequence variants (ASVs). The results of principal component analysis (PCA) and non-multidimensional scale analysis (nMDS) demonstrated the significant influence of wastewater treatment on both environmental factors and the microeukaryotic communities. Ciliophora was notably abundant in the effluent (42.09%) and sludge (17.11%). The aerobic stage was dominated by Ochrophyta, a diverse group of algae instrumental in nutrient removal, such as nitrogen and phosphorus, through biological processes. A redundancy analysis (RDA) revealed a positive correlation between chemical and biochemical oxygen demand and Cryptomycotina, highlighting its potential as a bioindicator for treatment efficacy. The detection of protozoan species, such as Acanthamoeba castellanii and Vermamoeba vermiformis, in the outlet stage poses health risks, whereas Cryptosporidium sp. was found in both the inlet and aerobic stages but not in the outlet. Our study reveals the complex nature of microeukaryotic diversity in the wastewater treatment system and its implications for treatment performance and public health.

Microbial Eukaryotes in Natural and Artificial Salt Marsh Pools

Microscopic eukaryotes are important components of coastal wetland ecosystems. The goal of this study was to investigate the diversity of microeukaryotes in the tidal pools of a New Jersey salt marsh and to compare the assemblages of natural and artificial pools excavated for controlling mosquito populations. We evaluated microeukaryotic assemblages using the amplicon sequencing of 18S and rbcL DNA markers and the microscopic identification of diatoms in water and sediment samples. 18S unique amplicon sequence variants (ASV) representing ciliates, dinoflagellates, diatoms, and cercozoans were the most diverse, while the reads of dinoflagellates, diatoms, ciliates, and nematodes were the most abundant. The dominant ASVs were attributed to organisms that are characteristic of coastal plankton and sediments or those known for their resistance to salinity, desiccation, hypoxia, and UV stress. The sediment assemblages were more diverse compared to those from the water column and contained a larger portion of ASVs that were not assigned to any low-rank taxa, reflecting the current gaps in understanding the diversity of microeukaryotes. Most taxonomic groups were significantly different in their abundance and composition between natural and artificial pools. Dinoflagellates, haptophytes, chrysophytes, pelagophytes, and raphidophytes—the groups that include a large proportion of mixotrophic taxa and species known for forming harmful algal blooms—were more abundant in the artificial than in the natural pools. Fungi, labyrinthulomycetes, and peronosporomycetes were also more abundant in artificial pools, which may be related to organic matter enrichment. Diatoms and foraminifera showed an opposite trend of higher abundance in natural pools.

Small Farm Holder Cropping Systems Influence Microbial Profiles in an Equatorial Rainforest Agroecosystem

The metabarcoding of prokaryotic and fungal (Ascomycota only) ribosomal DNA was used to describe the microbial communities in soils of a remnant equatorial rainforest, maize–bean intercrop, and sugarcane in western Kenya. Cropping systems influenced the microbial community composition and functional traits (energy source and nutrient cycling) of bulk soil in each crop. Microbial richness and diversity tended to increase with cultivation intensity. The soil of the maize–bean intercrop had lower percentages and sugarcane had higher percentages of unique amplicon sequence variants of both bacteria and fungi compared to the remnant forest. Functional traits were altered by cultivation intensity. Compared to remnant forest soils, maize–bean intercrop soil had lower percentages of aerobic chemoheterotrophic bacteria and higher percentages of N-cycling bacteria, while sugarcane had higher percentages of aerobic chemoheterotrophic bacteria and lower percentages of N-cycling bacteria. In the face of increasing forest loss and pressures for agricultural productivity, this landscape provides a rich site for studying the impacts of cropping systems on soil health.

Effects of the diet enrichment with β-glucan, sodium salt of butyric acid and vitamins on growth parameters and the profile of the gut microbiome of juvenile African catfish (Clarias gariepinus)

This study assessed the effect of the addition of active substances, i.e., β-glucan, sodium butyrate and vitamins (C, A, D3, E, K) to the diet of juvenile African catfish (Clarias gariepinus) on growth parameters and the intestinal microbiome. For this purpose, a four-week rearing of juveniles African catfish in a recirculating aquaculture system (RAS) under controlled conditions at 25°C was conducted. The fish were fed commercial feed (control group - C), which was enriched with various levels of sodium butyrate and β-glucan (FQV1 – FQV4). After the experiment, growth parameters such as weight gain (WG; g), length gain (LG; cm), specific growth rate (SGR; % d−1), condition factor (K) survival rate (SR; %) and cannibalism factor (CF; %) were determined. The profile of the intestinal microbiome was also determined using Next-Generation Sequencing (NGS) based on the analysis of the 16 S rRNA subunit. The obtained results indicated that feed supplementation with active substances in appropriate doses had a positive effect on the growth parameters of tested fish. Compared to the control group, statistically significant differences were obtained in WG (C - 7.62 g; FQV3 - FQV1 respectively 12.2–16.65 g), in WL (C - 6.23 cm; FQV3 - FQV1 respectively 7.59–8.74 cm), in SGR (C - 4.7%/d; FQV3 – V1 respectively 12.20 – 16.65 g), in K (C – 0.76; V3 – FQV4 respectively 0.80 – 0.84) (P <0.05). In addition, the control group had the highest value of CF (8.0%) compared to the research groups (P <0.05). The values of α-diversity metrics did not show statistically significant differences. However, the number of unique amplicon sequence variants (ASVs) in research groups confirmed that enriching the diet with the active substances increases the biodiversity of intestinal microbiome (C - 203; FQV4 - 373). In research groups and the control group, Firmicutes and Proteobacteria dominated, additionally, an increased number of beneficial lactic acid bacteria (LAB) of the Lactococcus and Bacillus genus was observed, while the number of potentially pathogenic bacteria of the Candidatus genus was reduced (P <0.05). Principal coordinate analysis (PCoA) determining β-diversity showed that the FQV3 was characterized by varied species composition compared to the other groups. The obtained results showed that a carefully selected composition of active ingredients used in the diet of juvenile African catfish has a beneficial effect on the profile and biodiversity of the intestinal microbiome, which indirectly improves resistance to infections and increases breeding indicators.

Comparative profiling of the skin and gut microbiota during metamorphosis in Chinese spiny frogs (Quasipaa spinosa) highlights microbial communities involved in disease pathogenesis

The symbiotic microbiota inhabiting the skin and gut of amphibians exerts roles in maintaining host health, especially during the critical stage of complete metamorphosis where failure to remodel the microbiota can result in various diseases. However, the composition and alterations in the amphibian microbiota in diverse diseased populations, as well as the exact mechanisms underlying disruptions in skin and gut microbial communities leading to diseases, are not yet well established. Herein, skin and gut microbiota were sampled from healthy Chinese spiny frogs (CTL group) as well as individuals with ascites disease (AD group), cataract disease (CD group), and rotten-skin disease (RD group) for Illumina high-throughput sequencing analysis to comprehensively explore potential associations between microbiota composition and the health status of the host. Venn diagrams and UpSet analysis revealed that the CTL group exhibited the highest number of unique amplicon sequence variants (ASVs) in their skin, while the CD group displayed the lowest abundance of ASVs in their gut. Compared to the CTL group, the alpha-diversity of skin microbiota was dramatically depressed in diseased groups, and notable variations in the beta-diversity of both skin and gut microbiota were observed. Further compositional analysis identified Firmicutes, Proteobacteria, and Bacteroidota as the dominant bacterial phyla in both skin and gut microbiota, although their relative abundances varied widely among groups. The linear discriminant analysis effect size (LEfSe) analysis identified various bacteria species with substantial differences between skin and gut microbiota groups including beneficial populations as well as opportunistic ones. Functional predictions indicated significant differences between CTL and diseased groups mainly enriched in metabolism-relevant pathways. Furthermore, in vitro culture experiments confirmed the presence of a total of 19 strains of bacteria from the skin microbiota of RD group, including opportunistic bacteria population Acinetobacter closely associated with spiny frog rotten-skin disease. Taken together, this work provides insights into the composition dynamics of skin and gut microbiota under different health conditions in spiny frogs, highlighting potential applications for symbiotic microbiota modification in promoting healthy amphibian culture practices as well as preventing diseases.

Soil nutrient management influences diversity, community association and functional structure of rhizosphere bacteriome under vegetable crop production.

Rhizosphere bacterial communities play a crucial role in promoting plant and soil ecosystem health and productivity. They also have great potential as key indicators of soil health in agroecosystems. Various environmental factors affect soil parameters, which have been demonstrated to influence soil microbial growth and activities. Thus, this study investigated how rhizosphere bacterial community structure and functions are affected by agronomic practices such as organic and conventional fertiliser application and plant species types. Rhizosphere soil of vegetable crops cultivated under organic and conventional fertilisers in different farms was analysed using high-throughput sequencing of the 16S rRNA gene and co-occurrence network pattern among bacterial species. The functional structure was analysed with PICRUSt2 pipeline. Overall, rhizosphere bacterial communities varied in response to fertiliser type, with soil physicochemical parameters, including NH4, PO4, pH and moisture content largely driving the variations across the farms. Organic farms had a higher diversity richness and more unique amplicon sequence variants than conventional farms. Bacterial community structure in multivariate space was highly differentiated across the farms and between organic and conventional farms. Co-occurrence network patterns showed community segmentation for both farms, with keystone taxa more prevalent in organic than conventional farms. Module hub composition and identity varied, signifying differences in keystone taxa across the farms and positive correlations between changes in microbial composition and ecosystem functions. The organic farms comprised functionally versatile communities characterised by plant growth-promoting keystone genera, such as Agromyces, Bacillus and Nocardioides. The results revealed that organic fertilisers support high functional diversity and stronger interactions within the rhizosphere bacterial community. This study provided useful information about the overall changes in soil microbial dynamics and how the changes influence ecosystem functioning under different soil nutrient management and agronomic practices.

Symbiont Identity Impacts the Microbiome and Volatilome of a Model Cnidarian-Dinoflagellate Symbiosis.

The symbiosis between cnidarians and dinoflagellates underpins the success of reef-building corals in otherwise nutrient-poor habitats. Alterations to symbiotic state can perturb metabolic homeostasis and thus alter the release of biogenic volatile organic compounds (BVOCs). While BVOCs can play important roles in metabolic regulation and signalling, how the symbiotic state affects BVOC output remains unexplored. We therefore characterised the suite of BVOCs that comprise the volatilome of the sea anemone Exaiptasia diaphana ('Aiptasia') when aposymbiotic and in symbiosis with either its native dinoflagellate symbiont Breviolum minutum or the non-native symbiont Durusdinium trenchii. In parallel, the bacterial community structure in these different symbiotic states was fully characterised to resolve the holobiont microbiome. Based on rRNA analyses, 147 unique amplicon sequence variants (ASVs) were observed across symbiotic states. Furthermore, the microbiomes were distinct across the different symbiotic states: bacteria in the family Vibrionaceae were the most abundant in aposymbiotic anemones; those in the family Crocinitomicaceae were the most abundant in anemones symbiotic with D. trenchii; and anemones symbiotic with B. minutum had the highest proportion of low-abundance ASVs. Across these different holobionts, 142 BVOCs were detected and classified into 17 groups based on their chemical structure, with BVOCs containing multiple functional groups being the most abundant. Isoprene was detected in higher abundance when anemones hosted their native symbiont, and dimethyl sulphide was detected in higher abundance in the volatilome of both Aiptasia-Symbiodiniaceae combinations relative to aposymbiotic anemones. The volatilomes of aposymbiotic anemones and anemones symbiotic with B. minutum were distinct, while the volatilome of anemones symbiotic with D. trenchii overlapped both of the others. Collectively, our results are consistent with previous reports that D. trenchii produces a metabolically sub-optimal symbiosis with Aiptasia, and add to our understanding of how symbiotic cnidarians, including corals, may respond to climate change should they acquire novel dinoflagellate partners.

Xylocopa caerulea and Xylocopa auripennis harbor a homologous gut microbiome related to that of eusocial bees.

Eusocial bees, such as bumblebees and honey bees, harbor host-specific gut microbiota through their social behaviors. Conversely, the gut microbiota of solitary bees is erratic owing to their lack of eusocial activities. Carpenter bees (genus Xylocopa) are long-lived bees that do not exhibit advanced eusociality like honey bees. However, they often compete for nests to reproduce. Xylocopa caerulea and Xylocopa auripennis are important pollinators of wild plants on Hainan Island. Whether they have host-specific bacteria in their guts similar to eusocial bees remains unknown. We targeted the bacterial 16S rRNA V3-V4 region to investigate the diversity of bacterial symbionts in the fore-midgut and hindgut of two carpenter bees, X. caerulea and X. auripennis. A maximum of 4,429 unique amplicon sequence variants (ASVs) were detected from all samples, belonging to 10 different phyla. X. caerulea and X. auripennis shared similar bacterial community profiles, with Lactobacillaceae, Bifidobacteriaceae, and Orbaceae being dominant in their entire guts. X. caerulea and X. auripennis harbor a highly conserved core set of bacteria, including the genera Candidatus Schmidhempelia and Bombiscardovia. These two bacterial taxa from carpenter bees are closely related to those isolated from bumblebees. The LEfSe analysis showed that Lactobacillaceae, Bifidobacteriaceae, and the genus Bombilactobacillus were significantly enriched in the hindguts of both carpenter bees. Functional prediction suggested that the most enriched pathways were involved in carbohydrate and lipid metabolism. Our results revealed the structure of the gut microbiota in two carpenter bees and confirmed the presence of some core bacterial taxa that were previously only found in the guts of social bees.

Quercus rubra invasion of temperate deciduous forest stands alters the structure and functions of the soil microbiome

Invasive plants can modify the diversity and taxonomical structure of soil microbiomes. However, it is difficult to generalize the underlying factors as their influence often seems to depend on the complex plant-soil-microbial interactions. In this paper, we investigated how Quercus rubra impacts on the soil microbiome across two soil horizons in relation to native woodland. Five paired adjacent invaded vs native vegetation plots in a managed forest in southern Poland were investigated. Soil microbial communities were assessed along with soil enzyme activities and soil physicochemical parameters, separately for both organic and mineral horizons, as well as forest stand characteristics to explore plant-soil-microbe interactions. Although Q. rubra did not significantly affect pH, organic C, total N, available nutrients nor enzymatic activity, differences in soil abiotic properties (except C to N ratio) were primarily driven by soil depth for both vegetation types. Further, we found significant differences in soil microbiome under invasion in relation to native vegetation. Microbial richness and diversity were lower in both horizons of Q. rubra vs control plots. Moreover, Q. rubra increased relative abundance of unique amplicon sequence variants in both horizons and thereby significantly changed the structure of the core soil microbial communities, in comparison to the control plots. In addition, predicted microbial functional groups indicated a predominant soil depth effect in both vegetation plots with higher abundance of aerobic chemoheterotrophic bacteria and endophytic fungi in the organic horizon and greater abundance of methanotrophic and methylotrophic bacteria, and ectomycorrhizal fungi in the mineral horizon. Overall, our results indicate strong associations between Q. rubra invasion and changes in soil microbiome and associated functions, a finding that needs to be further investigated to predict modifications in ecosystem functioning caused by this invasive species.

High replacement of fishmeal by Chlorella meal affects intestinal microbiota and the potential metabolic function in largemouth bass (Micropterus salmoides).

Microalgae have beneficial effects on the performance of fish as additives and they are becoming a promising alternative to fishmeal as macronutrient ingredients. However, the impact on the fish intestinal microbiome and the function, caused by microalgae as protein sources in diets, remains unclear. This study aimed to determine the composition and potential function of the intestinal microbial community of largemouth bass (Micropterus salmoides) fed diets at five replacement levels (0, 25, 50, 75 and 100%) of fishmeal by Chlorella meal in a basal diet (400 g kg−1) after 8 weeks. The results showed significant decreases in unique amplicon sequence variants in the intestine at the higher levels of fishmeal replacement. At 50% of fishmeal replacement, dietary inclusions of Chlorella meal had no impact on species richness and Shannon diversity and the community structure of the intestinal microbiota. However, high levels of fishmeal replacement (75 and 100%) significantly induced intestinal community disturbance and diversity loss in largemouth bass. Responding to the high fishmeal replacement level, the dominant genus Cetobacterium and Pleslomonas sharply increased and several taxa from Lactobacillus decreased significantly. Functional data predicted by PICRUSt revealed that nutrition-related metabolism was dominant in the intestinal microbiota of fish fed all the five diets, although some potential functions, particularly amino acid and lipid metabolisms, and energy metabolism, were upregulated firstly, and then downregulated in fish fed diets with the increase of dietary Chlorella meal. Meanwhile, certain pathways were not enriched in intestinal microbiome until up to 75% of fishmeal replacement, such as carbohydrate metabolism, and cofactors and vitamins metabolism. To conclude, this study reveals that fishmeal replacement (50%) by Chlorella meal at the level of 237 g kg−1 in diets is feasible for largemouth bass without impairing the microbiome structure and the metabolism function, providing an alternative strategy for evaluating the possibility of fishmeal replacement by microalgae in aquafeeds.

The healthy equine uterus harbors a distinct core microbiome plus a rich and diverse microbiome that varies with geographical location

The goal of this study was to understand the composition and existence of the resident uterine microbiome in healthy mares and to establish the presence of a core microbiome for the healthy equine uterus. We analyzed the microbiomes of 35 healthy mares that are long-time residents of three farms in Oklahoma, Louisiana, and Australia as well as that of 19 mares purchased from scattered owners in the Southern Mid-Western states of the United States. Over 6 million paired-end reads of the V4 region of the 16S rRNA gene were obtained resulting in 19,542 unique Amplicon Sequence Variants (ASVs). ASVs were assigned to 17 known phyla and 213 known genera. Most abundant genera across all animals were Pseudomonas (27%) followed by Lonsdalea (8%), Lactobacillus (7.5%), Escherichia/Shigella (4.5%), and Prevotella (3%). Oklahoma and Louisiana samples were dominated by Pseudomonas (75%). Lonsdalea (28%) was the most abundant genus in the Australian samples but was not found in any other region. Microbial diversity, richness, and evenness of the equine uterine microbiome is largely dependent on the geographical location of the animal. However, we observed a core uterine microbiome consisting of Lactobacillus, Escherichia/Shigella, Streptococcus, Blautia, Staphylococcus, Klebsiella, Acinetobacter, and Peptoanaerobacter.

Unravelling Stratified Microbial Assemblages in Australia’s Only Deep Anchialine System, The Bundera Sinkhole

Bundera sinkhole, located in north-western Australia, is the only known continental anchialine system in the Southern Hemisphere. Anchialine environments are characterised by stratified water columns with complex physicochemical profiles spanning hypoxic and anoxic regions, often displaying high levels of endemism. Research on these systems has focused on eukaryotic fauna, however interest in the microbial diversity of these environments is growing, enabled by next-generation DNA sequencing. Here we report detailed analyses of the microbial communities across a depth profile within Bundera sinkhole (from 2 to 28 m), involving parallel physicochemical measurements, cell population counts and 16S rRNA amplicon analyses. We observed clear shifts in microbial cell counts, community diversity, structure and membership across the depth profile, reflecting changing levels of light, organic and inorganic energy sources as well as shifts in pH and salinity. While Proteobacteria were the most abundant phylum found, there was a high degree of taxonomic novelty within these microbial communities, with 13,028 unique amplicon sequence variants (ASVs) identified, belonging to 67 identifiable bacterial and archaeal phyla. Of these ~4,600, more than one third of the total, were unclassified below family level. A small number of ASVs were highly abundant at select depths, all of which were part of the set not classified below family level. The 2 m and 6 m samples had in common two highly abundant ASVs, belonging to the Ectothiorhodospiraceae and Thiotrichaceae families, while the 8 m community contained a single predominant ASV belonging to family Thioglobaceae. At lower depths a different Ectothiorhodospiraceae ASV comprised up to 68% relative abundance, peaking at 26 and 28 m. Canonical correspondence analyses indicated that community structure was strongly influenced by differences in key physicochemical parameters, particularly salinity, dissolved organic and inorganic carbon, phosphate and sulphate concentrations. This work highlights the potential for anchialine systems to house considerable microbial novelty, potentially driven by adaptations to the specific physicochemical makeup of their local environment. As only a small number of anchialine systems have been examined via microbial community studies to date, this work is particularly valuable, contributing new insight regarding the microbial residents of these important and sensitive environments.

Alveolates (dinoflagellates, ciliates and apicomplexans) and Rhizarians are the most common microbial eukaryotes in temperate Appalachian karst caves.

SummaryThe purpose of this study was to survey the eukaryotic microbiome of two karst caves in the Valley and Ridge physiographic region of the Appalachian Mountains. Caves are known to harbour eukaryotic microbes but their very low densities and small cell size make them difficult to collect and identify. Microeukaryotes were surveyed using two methodologies, filtering water and submerging glass microscope slides mounted in periphytometers in cave pools. The periphyton sampling yielded 13.5 times more unique amplicon sequence variants (ASVs) than filtered water. The most abundant protist supergroup was Alveolata with large proportions of the ASVs belonging to dinoflagellate, ciliate and apicomplexan clades. The next most abundant were Rhizarians followed by Stramenopiles (diatoms and chrysophytes) and Ameobozoans. Very few of the ASVs, 1.5%, matched curated protist sequences with greater than 99% identity and only 2.5% could be identified from surface plankton samples collected in the same region. The overall composition of the eukaryotic microbiome appears to be a combination of bacterial grazers and parasitic species that could possibly survive underground as well as cells, cysts and spores probably transported from the surface.

Antarctic Hairgrass Rhizosphere Microbiomes: Microscale Effects Shape Diversity, Structure, and Function.

The rhizosphere microbiome of the native Antarctic hairgrass Deschampsia antarctica from the central maritime Antarctic was investigated using 16S RNA metagenomics and compared to those of the second native Antarctic plant Colobanthus quitensis and closely related temperate D. cespitosa. The rhizosphere microbial communities of D. antarctica and D. cespitosa had high taxon richness, while that of C. quitensis had markedly lower diversity. The majority of bacteria in the rhizosphere communities of the hairgrass were affiliated to Proteobacteria, Bacteroidetes, and Actinobacteria. The rhizosphere of C. quitensis was dominated by Actinobacteria. All microbial communities included high proportions of unique amplicon sequence variants (ASVs) and there was high heterogeneity between samples at the ASV level. The soil parameters examined did not explain this heterogeneity. Bacteria belonging to Actinobacteria, Bacteroidetes, and Proteobacteria were sensitive to fluctuations in the soil surface temperature. The values of the United Soil Surface Temperature Influence Index (UTII, Iti) showed that variations in most microbial communities from Galindez Island were associated with microscale variations in temperature. Metabolic predictions in silico using PICRUSt 2.0, based on the taxonomically affiliated part of the microbiomes, showed similarities with the rhizosphere community of D. antarctica in terms of the predicted functional repertoire. The results obtained indicate that these communities are involved in the primary processes of soil development (particularly the degradation of lignin and lignin-derived compounds) in the central maritime Antarctic and may be beneficial for the growth of Antarctic vascular plants. However, due to the limitations associated with interpreting PICRUSt 2.0 outputs, these predictions need to be verified experimentally.

Gut Microbiome of Wild Baltic Salmon (Salmo salar L.) Parr.

Gut microbiota of wild Baltic salmon (a sub-population of Atlantic salmon Salmo salar L.) parr was first analyzed using microbial profiling of the 16S rRNA gene (V3-V4 region) and high taxonomic richness was revealed. At the phylum level, the gut microbiota was dominated by Firmicutes, Actinobacteria, and Proteobacteria, the most numerous of which were Firmicutes. The phylum Tenericutes (mainly assigned to Mycoplasmataceae), which is common both in wild North- and East- Atlantic salmon parr, was not detected in Baltic salmon parr. Across all samples, unique amplicon sequence variants (ASVs) belonging to the unclassified Bacilli, Actinomycetales, and Rhizobiales were identified as the major taxa. Fifteen ASVs at the family level were found in all gut samples of Baltic salmon parr, the majority of which were Mycobacteriaceae, Cryptosporangiaceae, Microbacteriaceae, and Planctomycetaceae. At the genus level, Mycobacterium, Clostridium sensu stricto, and Hyphomicrobium were dominant but at low levels in all gut samples. Our study has revealed that the gut microbial community of wild Baltic salmon parr differs from those of wild North- and East-Atlantic salmon parr. This can be due to biogeographical differences or host-selective pressures, as the Baltic salmon population is believed to have split from the Atlantic salmon population in the Ancylian period.

Heterogeneity of Microbial Communities in Soils From the Antarctic Peninsula Region.

Ice-free areas represent less than 1% of the Antarctic surface. However, climate change models predict a significant increase in temperatures in the coming decades, triggering a relevant reduction of the ice-covered surface. Microorganisms, adapted to the extreme and fluctuating conditions, are the dominant biota. In this article we analyze the diversity and composition of soil bacterial communities in 52 soil samples on three scales: (i) fine scale, where we compare the differences in the microbial community between top-stratum soils (0–2 cm) and deeper-stratum soils (5–10 cm) at the same sampling point; (ii) medium scale, in which we compare the composition of the microbial community of top-stratum soils from different sampling points within the same sampling location; and (iii) coarse scale, where we compare communities between comparable ecosystems located hundreds of kilometers apart along the Antarctic Peninsula. The results suggest that in ice-free soils exposed for longer periods of time (millennia) microbial communities are significantly different along the soil profiles. However, in recently (decades) deglaciated soils the communities are not different along the soil profile. Furthermore, the microbial communities found in soils at the different sampling locations show a high degree of heterogeneity, with a relevant proportion of unique amplicon sequence variants (ASV) that appeared mainly in low abundance, and only at a single sampling location. The Core90 community, defined as the ASVs shared by 90% of the soils from the 4 sampling locations, was composed of 26 ASVs, representing a small percentage of the total sequences. Nevertheless, the taxonomic composition of the Core80 (ASVs shared by 80% of sampling points per location) of the different sampling locations, was very similar, as they were mostly defined by 20 common taxa, representing up to 75.7% of the sequences of the Core80 communities, suggesting a greater homogeneity of soil bacterial taxa among distant locations.