Community ecology across bacteria, archaea and microbial eukaryotes in the sediment and seawater of coastal Puerto Nuevo, Baja California

Ecological restoration reduces greenhouse gas emissions by altering planktonic and sedimentary microbial communities in a shallow eutrophic lake

Ecological restoration is a promising approach to alleviate eutrophication. However, its impacts on greenhouse gas (GHG) emissions and the underlying microbial mechanisms in different habitats of lakes remain unclear. To address this knowledge gap, we measured carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) fluxes at both water-air and sediment-water interfaces of eutrophic (Caohai) and restored area (Dapokou) of Dianchi Lake, a typical eutrophic lake in China. Meanwhile, we investigated the responses of planktonic and sedimentary bacterial and fungal communities by high-throughput sequencing. Our results indicated that 6 years of ecological restoration significantly reduced CO2 and N2O fluxes by 1.0-3.6 and 2.2-2.8 folds respectively, with more pronounced variations at the water-air interface than the sediment-water interface. Ecological restoration also shifted the structures of planktonic bacterial and fungal communities remarkably, leading to a significant reduction in the relative abundances of Actinobacteriota (by 70.94%), Bacteroidota (by 61.65%), Planctomycetota (by 74.18%) and Chytridiomycota (by 95.44%). Correlation analyses further suggested that GHG fluxes at the water-air interface were significantly correlated with planktonic microbial community composition (P < 0.05), and the significant reduction of CO2 and N2O fluxes under ecological restoration could be attributed to the decreased abundances of organic matter decomposers (such as hgcI_clade, Sporichthyaceae and Acidibacter) and increased abundances of autotrophs (such as Hydrogenophaga and Cyanobium_PCC-6307) in water. Collectively, our findings verify the importance of ecological restoration in reducing GHG emissions in inland lake ecosystems, providing new insights for addressing global climate change and advancing carbon neutrality.

Archaea show different geographical distribution patterns compared to bacteria and fungi in Arctic marine sediments

Microorganisms dominate marine environments in the polar oceans and are known to harbor greater diversity and abundance than was once thought, and yet, little is known about their biogeographic distribution patterns in marine sediments at a broad spatial scale. In this study, we conducted extensive sampling of marine sediments along a latitudinal transect spanning 2500 km from the Bering Sea to the Arctic Ocean to investigate the geographical distribution patterns of bacteria, archaea, and fungi. Our findings revealed that the community similarities of bacteria and fungi decay at similar rates with increasing geographical distance (slope: -0.005 and -0.002), which are much lower than the decay rate of archaeal communities (slope: -0.012). Notably, microbial richness and community composition showed significant differences in the region of 75-80°N compared to other regions in 60-75°N. Salinity, temperature, pH, ammonium nitrogen, and total organic carbon are key factors that significantly affect microbial community variations. Furthermore, bacterial co-occurrence networks showed more complex interactions but lower modularity than fungal counterparts. This study provides crucial insights into the spatial distribution patterns of bacteria, archaea, and fungi in the Arctic marine sediments and will be critical for a better understanding of microbial global distribution and ecological functions.

Antarctic Geothermal Soils Exhibit an Absence of Regional Habitat Generalist Microorganisms

Active geothermal systems are relatively rare in Antarctica and represent metaphorical islands ideal to study microbial dispersal. In this study, we tested the macro-ecological concept that high dispersal rates result in communities being dominated by either habitat generalists or specialists by investigating the microbial communities on four geographically separated geothermal sites on three Antarctic volcanoes (Mts. Erebus, Melbourne, and Rittman). We found that the microbial communities at higher temperature (max 65°C) sites (Tramway Ridge on Erebus and Rittmann) were unique from each other and were dominated by a variety of novel Archaea from class Nitrososphaeria, while lower temperature (max 50°C) sites (Western Crater on Erebus and Melbourne) had characteristically mesophilic communities (Planctomycetes, Acidobacteriota, etc.) that were highly similar. We found that 97% of the detected microbial taxa were regional habitat specialists, with no generalists, with community assembly driven by high dispersal rates and drift (25% and 30% of community assembly, respectively), not environmental selection. Our results indicate that for microbial communities experiencing high dispersal rates between isolated communities, habitat specialists may tend to out-compete habitat generalists.

Differential gut microbiota composition in β-Thalassemia patients and its correlation with iron overload

Recent research highlights the significant impact of the gut microbiota on health and disease. Thalassemia, a hereditary blood disorder, requires regular blood transfusions, leading to an accumulation of iron in the body. Such changes could potentially alter the intestinal microbiota, thereby increasing the susceptibility of thalassemic patients to infection. In this study, we analyzed the fecal microbiota of 70 non-transfusion-dependent (NTDT) β-thalassemia/HbE patients and 30 healthy controls. Our findings indicate that iron chelation intervention had no detectable effect on the microbiome profile of thalassemic patients. However, the cross-sectional analysis revealed that the bacterial diversity and community structure in patients were significantly less diverse and distinct compared to those of healthy subjects. Using reference frames, we were also able to demonstrate that bacterial taxa that are known to produce short chain fatty acids, from the genera Alistipes, Coprococcus, and Oscillospira, and those from the family Ruminococcaceae, were less prevalent in the patients. In contrast, bacterial taxa associated with an unhealthy gut, including the genus Clostridium and those from the families Fusobacteriaceae, Enterobacteriaceae, and Peptostrptococcaceae, were more prevalent in patients and found to be correlated with higher levels of ferritin. Collectively, these changes in the microbiota could be regarded as markers of raised ferritin levels, and therefore, awareness should be exercised as they could interfere, albeit indirectly, with the treatment of the co-morbidities of thalassemia.

Impacts of eutrophication on microbial community structure in sediment, seawater, and phyllosphere of seagrass ecosystems

Introduction

Seagrass-associated microbial communities play a crucial role in the growth and health of seagrasses. However, like seagrass meadows, seagrass-associated microbial communities are often affected by eutrophication. It remains unclear how eutrophication influences the composition and function of microbial communities associated with different parts of seagrass.

Methods

We employed prokaryotic 16S rRNA gene high-throughput sequencing combining microbial community structure analysis and co-occurrence network analysis to investigate variances in microbial community compositions, potential functions and complexities across sediment, seagrass leaves, and seawater within different eutrophic areas of two adjacent seagrass meadows on Hainan Island, China.

Results

Our results indicated that microbial diversity on seagrass leaves was significantly lower than in sediment but significantly higher than in seawater. Both sediment and phyllosphere microbial diversity showed no significant difference between the highly eutrophic and less eutrophic sites in each lagoon. However, sediment microbial diversity was higher in the more eutrophic lagoon, while phyllosphere microbial diversity was higher in the less eutrophic lagoon. Heavy eutrophication increased the relative abundance of phyllosphere microorganisms potentially involved in anaerobic metabolic processes, while reducing those responsible for beneficial functions like denitrification. The main factor affecting microbial diversity was organic carbon in seawater and sediment, with high organic carbon levels leading to decreased microbial diversity. The co-occurrence network analysis revealed that heavy eutrophication notably reduced the complexity and internal connections of the phyllosphere microbial community in comparison to the sediment and seawater microbial communities. Furthermore, ternary analysis demonstrated that heavy eutrophication diminished the external connections of the phyllosphere microbial community with the sediment and seawater microbial communities.

Conclusion

The pronounced decrease in biodiversity and complexity of the phyllosphere microbial community under eutrophic conditions can lead to greater microbial functional loss, exacerbating seagrass decline. This study emphasizes the significance of phyllosphere microbial communities compared to sediment microbial communities in the conservation and restoration of seagrass meadows under eutrophic conditions.

Carbapenem Resistance in Acinetobacter calcoaceticus-baumannii Complex Isolates From Kathmandu Model Hospital, Nepal, Is Attributed to the Presence of bla OXA-23-like and bla NDM-1 Genes

The Acinetobacter calcoaceticus-baumannii (ACB) complex, also known as ACB complex, consists of four bacterial species that can cause opportunistic infections in humans, especially in hospital settings. Conventional therapies for susceptible strains of the ACB complex include broad-spectrum cephalosporins, β-lactam/β-lactamase inhibitors, and carbapenems. Unfortunately, the effectiveness of these antibiotics has declined due to increasing rates of resistance. The predominant resistance mechanisms identified in the ACB complex involve carbapenem-resistant (CR) oxacillinases and metallo-β-lactamases (MBLs). This research, conducted at Kathmandu Model Hospital in Nepal, sought to identify genes associated with CR, specifically blaNDM-1, blaOXA-23-like, and blaOXA-24-like genes in carbapenem-resistant Acinetobacter calcoaceticus-baumannii (CR-ACB) complex. Additionally, the study is aimed at identifying the ACB complex through the sequencing of the 16s rRNA gene. Among the 992 samples collected from hospitalized patients, 43 (approximately 4.334%) tested positive for the ACB complex. These positive samples were mainly obtained from different hospital units, including intensive care units (ICUs); cabins; and neonatal, general, and maternity wards. The prevalence of infection was higher among males (58.14%) than females (41.86%), with the 40-50 age group showing the highest infection rate. In susceptibility testing, colistin and polymyxin B exhibited a susceptibility rate of 100%, whereas all samples showed resistance to third-generation cephalosporins. After polymyxins, gentamicin (30.23%) and amikacin (34.88%) demonstrated the highest susceptibility. A substantial majority (81.45%) of ACB complex isolates displayed resistance to carbapenems, with respiratory and pus specimens being the primary sources. Polymerase chain reaction (PCR) revealed that the primary CR gene within the ACB complex at this hospital was bla OXA-23-like, followed by bla NDM-1. To ensure the accuracy of the phenotypic assessment, 12 samples were chosen for 16s rRNA sequencing using Illumina MiSeq™ to confirm that they are Acinetobacter species. QIIME 2.0 analysis confirmed all 12 isolates to be Acinetobacter species. In the hospital setting, a substantial portion of the ACB complex carries CR genes, rendering carbapenem ineffective for treatment.

Relating gut microbiome composition and life history metrics for pronghorn (Antilocapra americana) in the Red Desert, Wyoming

Host microbial communities (hereafter, the 'microbiome') are recognized as an important aspect of host health and are gaining attention as a useful biomarker to understand the ecology and demographics of wildlife populations. Several studies indicate that the microbiome may contribute to the adaptive capacity of animals to changing environments associated with increasing habitat fragmentation and rapid climate change. To this end, we investigated the gut microbiome of pronghorn (Antilocapra americana), an iconic species in an environment that is undergoing both climatic and anthropogenic change. The bacterial composition of the pronghorn gut microbiome has yet to be described in the literature, and thus our study provides important baseline information about this species. We used 16S rRNA amplicon sequencing of fecal samples to characterize the gut microbiome of pronghorn-a facultative sagebrush (Artemisia spp.) specialist in many regions where they occur in western North America. We collected fecal pellets from 159 captured female pronghorn from four herds in the Red Desert of Wyoming during winters of 2013 and 2014. We found small, but significant differences in diversity of the gut microbiome relative to study area, capture period, and body fat measurements. In addition, we found a difference in gut microbiome composition in pronghorn across two regions separated by Interstate 80. Results indicated that the fecal microbiome may be a potential biomarker for the spatial ecology of free-ranging ungulates. The core gut microbiome of these animals-including bacteria in the phyla Firmicutes (now Bacillota) and Bacteroidota-remained relatively stable across populations and biological metrics. These findings provide a baseline for the gut microbiome of pronghorn that could potentially be used as a target in monitoring health and population structure of pronghorn relative to habitat fragmentation, climate change, and management practices.

Histone butyrylation in the mouse intestine is mediated by the microbiota and associated with regulation of gene expression

Post-translational modifications (PTMs) on histones are a key source of regulation on chromatin through impacting cellular processes, including gene expression1. These PTMs often arise from metabolites and are thus impacted by metabolism and environmental cues2-7. One class of metabolically regulated PTMs are histone acylations, which include histone acetylation, butyrylation, crotonylation and propionylation3,8. As these PTMs can be derived from short-chain fatty acids, which are generated by the commensal microbiota in the intestinal lumen9-11, we aimed to define how microbes impact the host intestinal chromatin landscape, mainly in female mice. Here we show that in addition to acetylation, intestinal epithelial cells from the caecum and distal mouse intestine also harbour high levels of butyrylation and propionylation on lysines 9 and 27 of histone H3. We demonstrate that these acylations are regulated by the microbiota and that histone butyrylation is additionally regulated by the metabolite tributyrin. Tributyrin-regulated gene programmes are correlated with histone butyrylation, which is associated with active gene-regulatory elements and levels of gene expression. Together, our study uncovers a regulatory layer of how the microbiota and metabolites influence the intestinal epithelium through chromatin, demonstrating a physiological setting in which histone acylations are dynamically regulated and associated with gene regulation.

Metatranscriptomics reveals diversity of symbiotic interaction and mechanisms of carbon exchange in the marine cyanolichen Lichina pygmaea

Lichens are exemplar symbioses based upon carbon exchange between photobionts and their mycobiont hosts. Historically considered a two-way relationship, some lichen symbioses have been shown to contain multiple photobiont partners; however, the way in which these photobiont communities react to environmental change is poorly understood. Lichina pygmaea is a marine cyanolichen that inhabits rocky seashores where it is submerged in seawater during every tidal cycle. Recent work has indicated that L. pygmaea has a complex photobiont community including the cyanobionts Rivularia and Pleurocapsa. We performed rRNA-based metabarcoding and mRNA metatranscriptomics of the L. pygmaea holobiont at high and low tide to investigate community response to immersion in seawater. Carbon exchange in L. pygmaea is a dynamic process, influenced by both tidal cycle and the biology of the individual symbiotic components. The mycobiont and two cyanobiont partners exhibit distinct transcriptional responses to seawater hydration. Sugar-based compatible solutes produced by Rivularia and Pleurocapsa in response to seawater are a potential source of carbon to the mycobiont. We propose that extracellular processing of photobiont-derived polysaccharides is a fundamental step in carbon acquisition by L. pygmaea and is analogous to uptake of plant-derived carbon in ectomycorrhizal symbioses.

Differential apicomplexan presence predicts thermal stress mortality in the Mediterranean coral Paramuricea clavata

Paramuricea clavata is an ecosystem architect of the Mediterranean temperate reefs that is currently threatened by episodic mass mortality events related to global warming. The microbiome may play an active role in the thermal stress susceptibility of corals, potentially holding the answer as to why corals show differential sensitivity to heat stress. To investigate this, the prokaryotic and eukaryotic microbiome of P. clavata collected from around the Mediterranean was characterised before experimental heat stress to determine if its microbial composition influences the thermal response of the holobiont. We found that members of P. clavata's microeukaryotic community were significantly correlated with thermal stress sensitivity. Syndiniales from the Dino-Group I Clade 1 were significantly enriched in thermally resistant corals, while the apicomplexan corallicolids were significantly enriched in thermally susceptible corals. We hypothesise that P. clavata mortality following heat stress may be caused by a shift from apparent commensalism to parasitism in the corallicolid-coral host relationship driven by the added stress. Our results show the potential importance of corallicolids and the rest of the microeukaryotic community of corals to understanding thermal stress response in corals and provide a useful tool to guide conservation efforts and future research into coral-associated microeukaryotes.

Effect of Ginger Root Powder on Gastrointestinal Bacteria Composition, Gastrointestinal Symptoms, Mental Health, Fatigue, and Quality of Life: A Double-Blind Placebo-Controlled Trial

BACKGROUND

Despite compositional alterations in gastrointestinal microbiota being purported to underpin some of the therapeutic effects of ginger, the effect of a standardized ginger supplement on gut microbiota has not been tested in humans.

OBJECTIVES

To determine the effect of a standardized ginger (Zingiber officinale) root powder, compared to placebo, on gastrointestinal bacteria and associated outcomes in healthy adults.

METHODS

A randomized double-blind placebo-controlled trial allocated participants aged 18 to 30 y to ginger or microcrystalline cellulose (MCC) placebo. The intervention comprised 1.2 g/d of ginger (4 capsules per day totaling 84 mg/d of active gingerols/shogaols) for 14 d following a 1-wk run-in period. Primary outcomes were gastrointestinal community composition, alpha and beta diversity, and differential abundance, measured using 16S rRNA gene sequencing of fecal samples. Secondary outcomes were gastrointestinal symptoms, bowel function, depression, anxiety, stress, fatigue, quality of life, and adverse events.

RESULTS

Fifty-one participants were enrolled and analyzed (71% female; mean age 25 ± 3 y; ginger: n = 29, placebo: n = 22). There was a greater increase in relative abundance of phylum, Actinobacteria, observed following ginger supplementation compared to placebo (U: 145.0; z: -2.1; P = 0.033). Ginger was associated with a greater abundance of the genera Parabacteroides, Bacillus, Ruminococcaceae incertae sedis, unclassified Bacilli, families Defluviitaleaceae, Morganellaceae, and Bacillaceae as well as lower abundance of the genus Blautia and family Sphingomonadaceae (P < 0.05). An improvement in indigestion symptoms was observed with ginger supplementation (U: 196.0; z: -2.4; P = 0.015). No differences between ginger and placebo groups were found for alpha and beta diversity or other secondary outcomes. No moderate or severe adverse events were reported.

CONCLUSIONS

Supplementation with ginger root powder was safe and altered aspects of gastrointestinal bacteria composition; however, it did not change alpha- or beta diversity, bowel function, gastrointestinal symptoms, mood, or quality of life in healthy adults. These results provide further understanding regarding the mechanisms of action of ginger supplementation. This trial was registered in the Australia New Zealand Clinical Trials Registry as ACTRN12620000302954p and the Therapeutic Goods Administration as CT-2020-CTN-00380-1.

Influence of organic plant breeding on the rhizosphere microbiome of common bean (Phaseolus vulgaris L.)

Introduction

We now recognize that plant genotype affects the assembly of its microbiome, which in turn, affects essential plant functions. The production system for crop plants also influences the microbiome composition, and as a result, we would expect to find differences between conventional and organic production systems. Plant genotypes selected in an organic regime may host different microbiome assemblages than those selected in conventional environments. We aimed to address these questions using recombinant inbred populations of snap bean that differed in breeding history.

Methods

Rhizosphere microbiomes of conventional and organic common beans (Phaseolus vulgaris L.) were characterized within a long-term organic research site. The fungal and bacterial communities were distinguished using pooled replications of 16S and ITS amplicon sequences, which originated from rhizosphere samples collected between flowering and pod set.

Results

Bacterial communities significantly varied between organic and conventional breeding histories, while fungal communities varied between breeding histories and parentage. Within the organically-bred populations, a higher abundance of a plant-growth-promoting bacteria, Arthrobacter pokkalii, was identified. Conventionally-bred beans hosted a higher abundance of nitrogen-fixing bacteria that normally do not form functional nodules with common beans. Fungal communities in the organically derived beans included more arbuscular mycorrhizae, as well as several plant pathogens.

Discussion

The results confirm that the breeding environment of crops can significantly alter the microbiome community composition of progeny. Characterizing changes in microbiome communities and the plant genes instrumental to these changes will provide essential information about how future breeding efforts may pursue microbiome manipulation.

Influence of submarine topography and sediment environment on microbial assemblages in a coastal lagoon in northeastern Japan

The relationships among eutrophication, anoxia, and microbial distribution were investigated for Nagatsura-Ura Lagoon on the northeastern Pacific coast of Japan. In September 2017, the bottom environment in a small area of the inner part of the lagoon (which has a basin-shaped bottom topology) was eutrophic and anoxic, with high carbon, nitrogen, phosphate, acid-volatile sulfide, and low dissolved oxygen and oxidation-reduction potential. Dissolved oxygen levels improved during the winter. Bacillariophyta (diatoms) were the main organic component according to pigment analysis and next-generation sequencing of nucleic acids in seawater samples. Phylum Proteobacteria was dominant among the bacterial flora in the sediment but the proportions of Class Epsilon-proteobacteria and Chlorobium (a green sulfur-utilizing bacterium) were high in the inner part of the lagoon compared to other stations, and these groups were also present in winter. Apparently groups able to thrive in both anoxic and aerobic conditions were predominant in the inner part of the lagoon.

Distinct assembly processes and environmental adaptation of abundant and rare archaea in Arctic marine sediments

Revealing the ecological processes and environmental adaptation of abundant and rare archaea is a central, but poorly understood, topic in ecology. Here, abundant and rare archaeal diversity, community assembly processes and co-occurrence patterns were comparatively analyzed in Arctic marine sediments. Our findings revealed that the rare taxa exhibited significantly higher diversity compared to the abundant taxa. Additionally, the abundant taxa displayed stronger environmental adaptation than the rare taxa. The co-occurrence network analysis demonstrated that the rare taxa developed more interspecies interactions and modules in response to environmental disturbance. Furthermore, the community assembly of abundant and rare taxa in sediments was primarily controlled by stochastic and deterministic processes, respectively. These findings provide valuable insights into the archaeal community assembly processes and significantly contribute to a deeper understanding of the environmental adaptability of abundant and rare taxa in Arctic marine sediments.

HIV Tat Expression and Cocaine Exposure Lead to Sex- and Age-Specific Changes of the Microbiota Composition in the Gut

The balance of microbial communities in the gut is extremely important for normal physiological function. Disruption of the balance is often associated with various disorders and diseases. Both HIV infection and cocaine use are known to change the gut microbiota and the epithelial barrier integrity, which contribute to inflammation and immune activation. Our recent study shows that Tat expression and cocaine exposure result in changes of genome-wide DNA methylation and gene expression and lead to worsen the learning and memory impairments. In the current study, we extended the study to determine effects of Tat and cocaine on the gut microbiota composition. We found that both Tat expression and cocaine exposure increased Alteromonadaceae in 6-month-old female/male mice. In addition, we found that Tat, cocaine, or both increased Alteromonadaceae, Bacteroidaceae, Cyanobiaceae, Erysipelotrichaceae, and Muribaculaceae but decreased Clostridiales_vadinBB60_group, Desulfovibrionaceae, Helicobacteraceae, Lachnospiraceae, and Ruminococcaceae in 12-month-old female mice. Lastly, we analyzed changes of metabolic pathways and found that Tat decreased energy metabolism and nucleotide metabolism, and increased lipid metabolism and metabolism of other amino acids while cocaine increased lipid metabolism in 12-month-old female mice. These results demonstrated that Tat expression and cocaine exposure resulted in significant changes of the gut microbiota in an age- and sex-dependent manner and provide additional evidence to support the bidirectional gut-brain axis hypothesis.

Sediment Microbiota as a Proxy of Environmental Health: Discovering Inter- and Intrakingdom Dynamics along the Eastern Mediterranean Continental Shelf

Sedimentary marine habitats are the largest ecosystem on our planet in terms of area. Marine sediment microbiota govern most of the benthic biological processes and therefore are responsible for much of the global biogeochemical activity. Sediment microbiota respond, even rapidly, to natural change in environmental conditions as well as disturbances of anthropogenic sources. The latter greatly impact the continental shelf. Characterization and monitoring of the sediment microbiota may serve as an important tool for assessing environmental health and indicate changes in the marine ecosystem. This study examined the suitability of marine sediment microbiota as a bioindicator for environmental health in the eastern Mediterranean Sea. Integration of information from Bacteria, Archaea, and Eukaryota enabled robust assessment of environmental factors controlling sediment microbiota composition: seafloor-depth (here representing sediment grain size and total organic carbon), core depth, and season (11%, 4.2%, and 2.5% of the variance, respectively). Furthermore, inter- and intrakingdom cooccurrence patterns indicate that ecological filtration as well as stochastic processes may control sediment microbiota assembly. The results show that the sediment microbiota was robust over 3 years of sampling, in terms of both representation of region (outside the model sites) and robustness of microbial markers. Furthermore, anthropogenic disturbance was reflected by significant transformations in sediment microbiota. We therefore propose sediment microbiota analysis as a sensitive approach to detect disturbances, which is applicable for long-term monitoring of marine environmental health. IMPORTANCE Analysis of data, curated over 3 years of sediment sampling, improves our understanding of microbiota assembly in marine sediment. Furthermore, we demonstrate the importance of cross-kingdom integration of information in the study of microbial community ecology. Finally, the urgent need to propose an applicable approach for environmental health monitoring is addressed here by establishment of sediment microbiota as a robust and sensitive model.

Stable isotope tracing in vivo reveals a metabolic bridge linking the microbiota to host histone acetylation

The gut microbiota influences acetylation on host histones by fermenting dietary fiber into butyrate. Although butyrate could promote histone acetylation by inhibiting histone deacetylases, it may also undergo oxidation to acetyl-coenzyme A (CoA), a necessary cofactor for histone acetyltransferases. Here, we find that epithelial cells from germ-free mice harbor a loss of histone H4 acetylation across the genome except at promoter regions. Using stable isotope tracing in vivo with 13C-labeled fiber, we demonstrate that the microbiota supplies carbon for histone acetylation. Subsequent metabolomic profiling revealed hundreds of labeled molecules and supported a microbial contribution to host fatty acid metabolism, which declined in response to colitis and correlated with reduced expression of genes involved in fatty acid oxidation. These results illuminate the flow of carbon from the diet to the host via the microbiota, disruptions to which may affect energy homeostasis in the distal gut and contribute to the development of colitis.

Ecological processes differ in community assembly of Archaea, Bacteria and Eukaryotes in a biogeographical survey of groundwater habitats in the Quebec region (Canada)

Aquifers are inhabited by microorganisms from the three major domains of life: Archaea, Eukaryotes and Bacteria. Although interest in the processes that govern the assembly of these microbial communities is growing, their study is almost systematically limited to one of the three domains of life. Archaea, Bacteria and Eukaryotes are however interconnected and essential to understand the functioning of their living ecosystems. We, therefore, conducted a spatial study of the distribution of microorganisms by sampling 35 wells spread over an area of 10,000 km² in the Quebec region (Canada). The obtained data allowed us to define the impact of geographic distance and geochemical water composition on the microbial communities. A null model approach was used to infer the relative influence of stochastic and determinist ecological processes on the assembly of the microbial community from all three domains. We found that the organisms from these three groups are mainly governed by stochastic mechanisms. However, this apparent similarity does not reflect the differences in the processes that govern the phyla assembly. The results obtained highlight the importance of considering all the microorganisms without neglecting their individual specificities.

Red Mangrove Propagule Bacterial Communities Vary With Geographic, But Not Genetic Distance

Bacterial communities associated with plant propagules remain understudied, despite the opportunities that propagules represent as dispersal vectors for bacteria to new sites. These communities may be the product of a combination of environmental influence and inheritance from parent to offspring. The relative role of these mechanisms could have significant implications for our understanding of plant-microbe interactions. We studied the correlates of microbiome community similarities across an invasion front of red mangroves (Rhizophora mangle L.) in Florida, where the species is expanding northward. We collected georeferenced propagule samples from 110 individuals of red mangroves across 11 populations in Florida and used 16S rRNA gene (iTag) sequencing to describe their bacterial communities. We found no core community of bacterial amplicon sequence variants (ASVs) across the Florida range of red mangroves, though there were some ASVs shared among individuals within most populations. Populations differed significantly as measured by Bray-Curtis dissimilarity, but not Unifrac distance. We generated data from 6 microsatellite loci from 60 individuals across 9 of the 11 populations. Geographic distance was correlated with beta diversity, but genetic distance was not. We conclude that red mangrove propagule bacterial communities are likely influenced more by local environmental acquisition than by inheritance.

Airborne Prokaryotic, Fungal and Eukaryotic Communities of an Urban Environment in the UK

Bioaerosols often contain human pathogens and allergens affecting public health. However, relatively little attention has been given to bioaerosols compared with non-biological aerosols. In this study, we aimed to identify bioaerosol compositions in Manchester, UK by applying high throughput sequencing methods and to find potential sources. Samples were collected at Manchester Air Quality Super Site at the Firs Environmental Research Station in November 2019 and in February 2020. Total DNA has been extracted and sequenced targeting the 16S rRNA gene of prokaryotes, ITS region of fungal DNA and 18S rRNA gene of eukaryotes. We found marine environment-associated bacteria and archaea were relatively more abundant in the February 2020 samples compared with the November 2019 samples, consistent with the North West marine origin based on wind back-trajectory analysis. In contrast, an OTU belonging to Methylobacterium, which includes many species resistant to heavy metals, was relatively more abundant in November 2019 when there were higher metal concentrations. Fungal taxa that fruit all year were relatively more abundant in the February 2020 samples while autumn fruiting species generally had higher relative abundance in the November 2019 samples. There were higher relative abundances of land plants and algae in the February 2020 samples based on 18S rRNA gene sequencing. One of the OTUs belonging to the coniferous yew genus Taxus was more abundant in the February 2020 samples agreeing with the usual pollen season of yews in the UK which is from mid-January until late April. The result from this study suggests a potential application of bioaerosol profiling for tracing the source of atmospheric particles.

The Functional Biogeography of eDNA Metacommunities in the Post-Fire Landscape of the Angeles National Forest

Wildfires have continued to increase in frequency and severity in Southern California due in part to climate change. To gain a further understanding of microbial soil communities’ response to fire and functions that may enhance post-wildfire resilience, soil fungal and bacterial microbiomes were studied from different wildfire areas in the Gold Creek Preserve within the Angeles National Forest using 16S, FITS, 18S, 12S, PITS, and COI amplicon sequencing. Sequencing datasets from December 2020 and June 2021 samplings were analyzed using QIIME2, ranacapa, stats, vcd, EZBioCloud, and mixomics. Significant differences were found among bacterial and fungal taxa associated with different fire areas in the Gold Creek Preserve. There was evidence of seasonal shifts in the alpha diversity of the bacterial communities. In the sparse partial least squares analysis, there were strong associations (r > 0.8) between longitude, elevation, and a defined cluster of Amplicon Sequence Variants (ASVs). The Chi-square test revealed differences in fungi−bacteria (F:B) proportions between different trails (p = 2 × 10−16). sPLS results focused on a cluster of Green Trail samples with high elevation and longitude. Analysis revealed the cluster included the post-fire pioneer fungi Pyronema and Tremella. Chlorellales algae and possibly pathogenic Fusarium sequences were elevated. Bacterivorous Corallococcus, which secretes antimicrobials, and bacterivorous flagellate Spumella were associated with the cluster. There was functional redundancy in clusters that were differently composed but shared similar ecological functions. These results implied a set of traits for post-fire resiliency. These included photo-autotrophy, mineralization of pyrolyzed organic matter and aromatic/oily compounds, potential pathogenicity and parasitism, antimicrobials, and N-metabolism.

Unique Geothermal Chemistry Shapes Microbial Communities on Mt. Erebus, Antarctica

Mt. Erebus, Antarctica, is the world's southernmost active volcano and is unique in its isolation from other major active volcanic systems and its distinctive geothermal systems. Using 16S rRNA gene amplicon sequencing and physicochemical analyses, we compared samples collected at two contrasting high-temperature (50°C-65°C) sites on Mt. Erebus: Tramway Ridge, a weather-protected high biomass site, and Western Crater, an extremely exposed low biomass site. Samples were collected along three thermal gradients, one from Western Crater and two within Tramway Ridge, which allowed an examination of the heterogeneity present at Tramway Ridge. We found distinct soil compositions between the two sites, and to a lesser extent within Tramway Ridge, correlated with disparate microbial communities. Notably, pH, not temperature, showed the strongest correlation with these differences. The abundance profiles of several microbial groups were different between the two sites; class Nitrososphaeria amplicon sequence variants (ASVs) dominated the community profiles at Tramway Ridge, whereas Acidobacteriotal ASVs were only found at Western Crater. A co-occurrence network, paired with physicochemical analyses, allowed for finer scale analysis of parameters correlated with differential abundance profiles, with various parameters (total carbon, total nitrogen, soil moisture, soil conductivity, sulfur, phosphorous, and iron) showing significant correlations. ASVs assigned to Chloroflexi classes Ktedonobacteria and Chloroflexia were detected at both sites. Based on the known metabolic capabilities of previously studied members of these groups, we predict that chemolithotrophy is a common strategy in this system. These analyses highlight the importance of conducting broader-scale metagenomics and cultivation efforts at Mt. Erebus to better understand this unique environment.

Eutrophication dangers the ecological status of coastal wetlands: A quantitative assessment by composite microbial index of biotic integrity

The intertidal wetland ecosystem is vulnerable to environmental and anthropogenic stressors. Understanding how the ecological statuses of intertidal wetlands respond to influencing factors is crucial for the management and protection of intertidal wetland ecosystems. In this study, the community characteristics of bacteria, archaea and microeukaryote from Jiangsu coast areas (JCA), the longest muddy intertidal wetlands in the world, were detected to develop a composite microbial index of biotic integrity (CM-IBI) and to explore the influence mechanisms of stresses on the intertidal wetland ecological status. A total of 12 bacterial, archaea and microeukaryotic metrics were determined by range, responsiveness and redundancy tests for the development of ba-IBI, ar-IBI and eu-IBI. The CM-IBI was further developed via three sub-IBIs with weight coefficients 0.40, 0.33 and 0.27, respectively. The CM-IBI (R² = 0.58) exhibited the highest goodness of fit with the CEI, followed by ba-IBI (R² = 0.36), ar-IBI (R² = 0.25) and eu-IBI (R² = 0.21). Redundancy and random forest analyses revealed inorganic nitrogen (inorgN), total phosphorus (TP) and total organic carbon (TOC) to be key environmental variables influencing community compositions. A conditional reasoning tree model indicated the close associating between the ecological status and eutrophication conditions. The majority of sites with water inorgN<0.67 mg/L exhibited good statuses, while the poor ecological status was observed for inorgN>0.67 mg/L and TP > 0.11 mg/L. Microbial networks demonstrated the interactions of microbial taxonomic units among three kingdoms decreases with the ecological degradation, suggesting a reduced reliability and stability of microbial communities. Multi-level path analysis revealed fishery aquaculture and industrial development as the dominant anthropogenic activities effecting the eutrophication and ecological degradation of the JCA tidal wetlands. This study developed an efficient ecological assessment method of tidal wetlands based on microbial communities, and determined the influence of human activities and eutrophication on ecological status, providing guidance for management standards and coastal development.

Sediment and their bacterial communities in an industrialized estuary after Hurricane Harvey

Estuaries experience variable physicochemical conditions, especially after hurricanes and due to anthropogenic sources of pollution. Their microbial communities are not as well understood in terms of community structure and diversity, particularly in response to stresses from pollution and severe events. This study presents a 16S rRNA-based description of sediment microbial communities in the Houston Ship Channel-Galveston Bay estuary after Hurricane Harvey in 2017. A total of 11 sites were sampled, and microbial genomic DNA was isolated from sediment. The presence and abundance of specific bacterial and archaeal taxa in the sediment indicated pollutant inputs from identified legacy sources. The abundance of certain microbial groups was explained by the mobilization of contaminated sediment and sediment transport due to Harvey. Several microorganisms involved in the biodegradation of xenobiotics were observed. The spatial occurrence of Dehalococcoidia, a degrader of persistent polychlorinated compounds, was explained in relation to sediment properties and contaminant concentrations.

Changes in the sediment microbial community structure of coastal and inland sinkholes of a karst ecosystem from the Yucatan peninsula

The karst underground river ecosystem of Yucatan peninsula is composed of cave systems and sinkholes. The microbial diversity of water from this underground river has been studied, but, structure of the microbial community in its cave sediments remained largely unknown. Here we describe how the microbial community structure of these sediments changes due to different environmental conditions found in sediment zones along the caves of a coastal and an inland sinkhole. We found that dominant microbial groups varied according to the type of sinkhole (Coastal: Chloroflexi and Crenarchaeota; inland: Methylomirabilota and Acidobacteriota) and that the community structures differed both among sinkhole types, and within the sediment zones that were studied. These microorganisms are associated with different types of metabolism, and differed from a microbial community dominated by sulfate reducers at the coastal sinkhole, to one dominated by methylotrophs at the inland sinkhole, suggesting there are biogeochemical processes in the coastal and inland sinkholes that lead to changes in the microbial composition of the underground river ecosystem's sediments. Our results suggest sediments from unexplored sinkhole caves are unique environmental niches with distinct microbial assemblages that putatively play an important role in the biogeochemical cycles of these ecosystems.

Metagenomic Insights into the Composition and Function of Microbes Associated with the Rootzone of Datura inoxia

The purpose of this paper is to elucidate the roles that microbes may be playing in the rootzone of the medicinal plant Daturainoxia. We hypothesized that the microbes associated with the Datura rootzone would be significantly different than the similar surrounding fields in composition and function. We also hypothesized that rhizospheric and endophytic microbes would be associated with similar metabolic functions to the plant rootzone they inhabited. The methods employed were microbial barcoding, tests of essential oils against antibiotic resistant bacteria and other soil bacterial isolates, 16S Next Generation Sequencing (NGS) metabarcoding, and Whole Genome Shotgun (WGS) taxonomic and functional analyses. A few of the main bacterial genera of interest that were differentially abundant in the Datura root microbiome were Flavobacterium (p = 0.007), Chitinophaga (p = 0.0007), Pedobacter (p = 6 × 10−5), Bradyhizobium (p = 1 × 10−8), and Paenibacillus (p = 1.46 × 10−6). There was significant evidence that the microbes associated with the Datura rootzone had elevated function related to bacterial chalcone synthase (p = 1.49 × 10−3) and permease genes (p < 0.003). There was some evidence that microbial functions in the Datura rootzone provided precursors to important plant bioactive molecules or were beneficial to plant growth. This is important because these compounds are phyto-protective antioxidants and are precursors to many aromatic bioactive compounds that are relevant to human health. In the context of known interactions, and current results, plants and microbes influence the flavonoid biosynthetic pathways of one other, in terms of the regulation of the phenylpropanoid pathway. This is the first study to focus on the microbial ecology of the Datura rootzone. There are possible biopharmaceutical and agricultural applications of the natural interplay that was discovered during this study of the Datura inoxia rhizosphere.

Breastmilk, Stool, and Meconium: Bacterial Communities in South Africa

Human milk optimizes gut microbial richness and diversity, and is critical for proper immune development. Research has shown differing microbial composition based on geographic location, providing evidence that diverse biospecimen data is needed when studying human bacterial communities. Yet, limited research describes human milk and infant gut microbial communities in Africa. Our study uses breastmilk, stool, and meconium samples from a South African birth cohort to describe the microbial diversity, identify distinct taxonomic units, and determine correlations between bacterial abundance in breastmilk and stool samples. Mother-infant dyads (N = 20) were identified from a longitudinal birth cohort in the Vhembe district of Limpopo Province, South Africa. Breastmilk, meconium, and stool samples were analyzed using 16S ribosomal RNA sequencing of the V4-V5 gene region using the MiSeq platform for identification and relative quantification of bacterial taxa. A non-metric multidimensional scaling using Bray-Curtis distances of sample Z-scores showed that meconium, stool, and breastmilk microbial communities are distinct with varying genus. Breastmilk was mostly comprised of Streptococcus, Staphylococcus, Veillonella, and Corynebacterium. Stool samples showed the highest levels of Bifidobacterium, Faecalibacterium, Bacteroides, and Streptococcus. Alpha diversity measures found that stool samples have the highest Shannon index score compared to breastmilk and meconium. The abundance of Bifidobacterium (r = 0.57), Blautia (r = 0.59), and Haemophilus (r = 0.69) was correlated (p < 0.1) between breastmilk and stool samples. Despite the importance of breastmilk in seeding the infant gut microbiome, we found evidence of distinct bacterial communities between breastmilk and stool samples from South African mother-infant dyads.

Inconsistent Patterns of Microbial Diversity and Composition Between Highly Similar Sequencing Protocols: A Case Study With Reef-Building Corals

16S rRNA gene profiling (amplicon sequencing) is a popular technique for understanding host-associated and environmental microbial communities. Most protocols for sequencing amplicon libraries follow a standardized pipeline that can differ slightly depending on laboratory facility and user. Given that the same variable region of the 16S gene is targeted, it is generally accepted that sequencing output from differing protocols are comparable and this assumption underlies our ability to identify universal patterns in microbial dynamics through meta-analyses. However, discrepant results from a combined 16S rRNA gene dataset prepared by two labs whose protocols differed only in DNA polymerase and sequencing platform led us to scrutinize the outputs and challenge the idea of confidently combining them for standard microbiome analysis. Using technical replicates of reef-building coral samples from two species, Montipora aequituberculata and Porites lobata, we evaluated the consistency of alpha and beta diversity metrics between data resulting from these highly similar protocols. While we found minimal variation in alpha diversity between platform, significant differences were revealed with most beta diversity metrics, dependent on host species. These inconsistencies persisted following removal of low abundance taxa and when comparing across higher taxonomic levels, suggesting that bacterial community differences associated with sequencing protocol are likely to be context dependent and difficult to correct without extensive validation work. The results of this study encourage caution in the statistical comparison and interpretation of studies that combine rRNA gene sequence data from distinct protocols and point to a need for further work identifying mechanistic causes of these observed differences.

The Methods of Digging for "Gold" within the Salt: Characterization of Halophilic Prokaryotes and Identification of Their Valuable Biological Products Using Sequencing and Genome Mining Tools

Halophiles, the salt-loving organisms, have been investigated for at least a hundred years. They are found in all three domains of life, namely Archaea, Bacteria, and Eukarya, and occur in saline and hypersaline environments worldwide. They are already a valuable source of various biomolecules for biotechnological, pharmaceutical, cosmetological and industrial applications. In the present era of multidrug-resistant bacteria, cancer expansion, and extreme environmental pollution, the demand for new, effective compounds is higher and more urgent than ever before. Thus, the unique metabolism of halophilic microorganisms, their low nutritional requirements and their ability to adapt to harsh conditions (high salinity, high pressure and UV radiation, low oxygen concentration, hydrophobic conditions, extreme temperatures and pH, toxic compounds and heavy metals) make them promising candidates as a fruitful source of bioactive compounds. The main aim of this review is to highlight the nucleic acid sequencing experimental strategies used in halophile studies in concert with the presentation of recent examples of bioproducts and functions discovered in silico in the halophile's genomes. We point out methodological gaps and solutions based on in silico methods that are helpful in the identification of valuable bioproducts synthesized by halophiles. We also show the potential of an increasing number of publicly available genomic and metagenomic data for halophilic organisms that can be analysed to identify such new bioproducts and their producers.

Skin-penetrating nematodes exhibit life-stage-specific interactions with host-associated and environmental bacteria

BACKGROUND

Skin-penetrating nematodes of the genus Strongyloides infect over 600 million people, posing a major global health burden. Their life cycle includes both a parasitic and free-living generation. During the parasitic generation, infective third-stage larvae (iL3s) actively engage in host seeking. During the free-living generation, the nematodes develop and reproduce on host feces. At different points during their life cycle, Strongyloides species encounter a wide variety of host-associated and environmental bacteria. However, the microbiome associated with Strongyloides species, and the behavioral and physiological interactions between Strongyloides species and bacteria, remain unclear.

RESULTS

We first investigated the microbiome of the human parasite Strongyloides stercoralis using 16S-based amplicon sequencing. We found that S. stercoralis free-living adults have an associated microbiome consisting of specific fecal bacteria. We then investigated the behavioral responses of S. stercoralis and the closely related rat parasite Strongyloides ratti to an ecologically diverse panel of bacteria. We found that S. stercoralis and S. ratti showed similar responses to bacteria. The responses of both nematodes to bacteria varied dramatically across life stages: free-living adults were strongly attracted to most of the bacteria tested, while iL3s were attracted specifically to a narrow range of environmental bacteria. The behavioral responses to bacteria were dynamic, consisting of distinct short- and long-term behaviors. Finally, a comparison of the growth and reproduction of S. stercoralis free-living adults on different bacteria revealed that the bacterium Proteus mirabilis inhibits S. stercoralis egg hatching, and thereby greatly decreases parasite viability.

CONCLUSIONS

Skin-penetrating nematodes encounter bacteria from various ecological niches throughout their life cycle. Our results demonstrate that bacteria function as key chemosensory cues for directing parasite movement in a life-stage-specific manner. Some bacterial genera may form essential associations with the nematodes, while others are detrimental and serve as a potential source of novel nematicides.

Profiling of Microbial Communities in the Sediments of Jinsha River Watershed Exposed to Different Levels of Impacts by the Vanadium Industry, Panzhihua, China

The mining, smelting, manufacturing, and disposal of vanadium (V) and associated products have caused serious environmental problems. Although the microbial ecology in V-contaminated soils has been intensively studied, the impacted watershed ecosystems have not been systematically investigated. In this study, geochemistry and microbial structure were analyzed along ~30 km of the Jinsha River and its two tributaries across the industrial areas in Panzhihua, one of the primary V mining and production cities in China. Geochemical analyses showed different levels of contamination by metals and metalloids in the sediments, with high degrees of contamination observed in one of the tributaries close to the industrial park. Analyses of the V4 hypervariable region of 16S rRNA genes of the microbial communities in the sediments showed significant decrease in microbial diversity and microbial structure in response to the environmental gradient (e.g., heavy metals, total sulfur, and total nitrogen). Strong association of the taxa (e.g., Thauera, Algoriphagus, Denitromonas, and Fontibacter species) with the metals suggested selection for these potential metal-resistant and/or metabolizing populations. Further co-occurrence network analysis showed that many identified potential metal-mediating species were among the keystone taxa that were closely associated in the same module, suggesting their strong inter-species interactions but relative independence from other microorganisms in the hydrodynamic ecosystems. This study provided new insight into the microbe-environment interactions in watershed ecosystems differently impacted by the V industries. Some of the phylotypes identified in the highly contaminated samples exhibited potential for bioremediation of toxic metals (e.g., V and Cr).

Nonalcoholic Steatohepatitis and HCC in a Hyperphagic Mouse Accelerated by Western Diet

BACKGROUND & AIMS

How benign liver steatosis progresses to nonalcoholic steatohepatitis (NASH), fibrosis, and hepatocellular carcinoma (HCC) remains elusive. NASH progression entails diverse pathogenic mechanisms and relies on complex cross-talk between multiple tissues such as the gut, adipose tissues, liver, and the brain. Using a hyperphagic mouse fed with a Western diet (WD), we aimed to elucidate the cross-talk and kinetics of hepatic and extrahepatic alterations during NASH-HCC progression, as well as regression.

METHODS

Hyperphagic mice lacking a functional Alms1 gene (Foz/Foz) and wild-type littermates were fed WD or standard chow for 12 weeks for NASH/fibrosis and for 24 weeks for HCC development. NASH regression was modeled by switching back to normal chow after NASH development.

RESULTS

Foz+WD mice were steatotic within 1 to 2 weeks, developed NASH by 4 weeks, and grade 3 fibrosis by 12 weeks, accompanied by chronic kidney injury. Foz+WD mice that continued on WD progressed to cirrhosis and HCC within 24 weeks and had reduced survival as a result of cardiac dysfunction. However, NASH mice that were switched to normal chow showed NASH regression, improved survival, and did not develop HCC. Transcriptomic and histologic analyses of Foz/Foz NASH liver showed strong concordance with human NASH. NASH was preceded by an early disruption of gut barrier, microbial dysbiosis, lipopolysaccharide leakage, and intestinal inflammation. This led to acute-phase liver inflammation in Foz+WD mice, characterized by neutrophil infiltration and increased levels of several chemokines/cytokines. The liver cytokine/chemokine profile evolved as NASH progressed, with subsequent predominance by monocyte recruitment.

CONCLUSIONS

The Foz+WD model closely mimics the pathobiology and gene signature of human NASH with fibrosis and subsequent HCC. Foz+WD mice provide a robust and relevant preclinical model of NASH, NASH-associated HCC, chronic kidney injury, and heart failure.

Comparing Sediment Microbiomes in Contaminated and Pristine Wetlands along the Coast of Yucatan

Microbial communities are important players in coastal sediments for the functioning of the ecosystem and the regulation of biogeochemical cycles. They also have great potential as indicators of environmental perturbations. To assess how microbial communities can change their composition and abundance along coastal areas, we analyzed the composition of the microbiome of four locations of the Yucatan Peninsula using 16S rRNA gene amplicon sequencing. To this end, sediment from two conserved (El Palmar and Bocas de Dzilam) and two contaminated locations (Sisal and Progreso) from the coast northwest of the Yucatan Peninsula in three different years, 2017, 2018 and 2019, were sampled and sequenced. Microbial communities were found to be significantly different between the locations. The most noticeable difference was the greater relative abundance of Planctomycetes present at the conserved locations, versus FBP group found with greater abundance in contaminated locations. In addition to the difference in taxonomic groups composition, there is a variation in evenness, which results in the samples of Bocas de Dzilam and Progreso being grouped separately from those obtained in El Palmar and Sisal. We also carry out the functional prediction of the metabolic capacities of the microbial communities analyzed, identifying differences in their functional profiles. Our results indicate that landscape of the coastal microbiome of Yucatan sediment shows changes along the coastline, reflecting the constant dynamics of coastal environments and their impact on microbial diversity.

Different distribution patterns of microorganisms between aquaculture pond sediment and water

Aquatic microorganisms in the sediment and water column are closely related; however, their distribution patterns between these two habitats still remain largely unknown. In this study, we compared sediment and water microeukaryotic and bacterial microorganisms in aquaculture ponds from different areas in China, and analyzed the influencing environmental factors as well as the inter-taxa relationships. We found that bacteria were significantly more abundant than fungi in both sediment and water, and the bacterial richness and diversity in sediment were higher than in water in all the sampling areas, but no significant differences were found between the two habitats for microeukaryotes. Bacterial taxa could be clearly separated through cluster analysis between the sediment and water, while eukaryotic taxa at all classification levels could not. Spirochaetea, Deltaproteobacteria, Nitrospirae, Ignavibacteriae, Firmicutes, Chloroflexi, and Lentimicrobiaceae were more abundantly distributed in sediment, while Betaproteobacteria, Alphaproteobacter, Cyanobacteria, Roseiflexaceae, Dinghuibacter, Cryomorphaceae, and Actinobacteria were more abundant in water samples. For eukaryotes, only Cryptomonadales were found to be distributed differently between the two habitats. Microorganisms in sediment were mainly correlated with enzymes related to organic matter decomposition, while water temperature, pH, dissolved oxygen, and nutrient levels all showed significant correlation with the microbial communities in pond water. Intensive interspecific relationships were also found among eukaryotes and bacteria. Together, our results indicated that eukaryotic microorganisms are distributed less differently between sediment and water in aquaculture ponds compared to bacteria. This study provides valuable data for evaluating microbial distributions in aquatic environments, which may also be of practical use in aquaculture pond management.

Direct Conversion of Food Waste Extract into Caproate: Metagenomics Assessment of Chain Elongation Process

In a circular economy strategy, waste resources can be used for the biological production of high added-value substances, such as medium chain fatty acids (MCFAs), thus minimising waste and favouring a sustainable process. This study investigates single-stage fermentation processes for the production of MCFAs in a semi-continuous reactor treating the extract of real food waste (FW), without the addition of external electron donors. Two sequential acidogenic fermentation tests were carried out at an organic loading rate (OLR) of 5 and 15 gCOD L⁻¹d⁻¹ with a hydraulic retention time of 4 days and pH controlled at 6 ± 0.2. The highest level of caproate (4.8 g L⁻¹) was observed at OLR of 15 gCOD L⁻¹d⁻¹ with a microbiome mainly composed by lactate-producing Actinomyces, Atopobium, and Olsenella species and caproate-producing Pseudoramibacter. Metagenomic analysis revealed the presence of key enzymes for the production of lactate, such as lactate dehydrogenase and pyruvate ferredoxin oxidoreductase, as well as several enzymes involved in the reverse β-oxidation pathway, thus suggesting the occurrence of a lactate-based chain elongation process.

Exploring the impacts of heavy metals on spatial variations of sediment-associated bacterial communities

One of the fundamental objectives in modern ecology is to decipher how bacterial communities in natural environment respond to anthropogenic activities. In recent times consequences of marine pollution, especially with heavy metals (HMs) have received increasing attention. However, insights into the response of bacterial communities to HMs in coastal sediments of India remain scarce. Here, we analyzed HMs content in three areas, along the southern coastal region of India. Based on the calculated pollution indices viz., enrichment factor (EF), contamination factor (CF), geo-accumulation index (Igeo) and sediment quality guidelines (SQGs), the studied areas were classified as uncontaminated, moderately contaminated and significantly contaminated. To explore the response of bacterial community to HMs, sediment-associated microbiota was investigated using high-throughput 16S rRNA gene amplicon sequencing. The obtained metataxonomic results revealed that bacterial diversity and community composition varied considerably in significantly contaminated area than moderately contaminated and uncontaminated areas. Proportion of bacterial classes was higher for Gammaproteobacteria, Betaproteobacteria and Actinobacteria, but lower for Alphaproteobacteria and Flavobacteriia in significantly contaminated area. Also, samples of significantly contaminated area were dominated by well-documented metal-resistant bacterial genera such as Ralstonia and Arthrobacter. Canonical correspondence analysis (CCA) showed that spatial variability of bacterial community composition was strongly correlated with HMs content such as Chromium, Cadmium and Nickel. Further analysis using PICRUSt programme indicated that the predictive functional profile also varied considerably in significantly contaminated area. By linking HMs with bacterial compositional variations, the present study highlights the likely influence of HMs in shaping sedimentary microbiota of coastal regions.

Characterization of sediment microbial communities at two sites with low hydrocarbon pollution in the southeast Gulf of Mexico

Background

Coastal ecosystems are prone to hydrocarbon pollution due to human activities, and this issue has a tremendous impact on the environment, socioeconomic consequences, and represents a hazard to humans. Bioremediation relies on the ability of bacteria to metabolize hydrocarbons with the aim of cleaning up polluted sites.

Methods

The potential of naturally occurring microbial communities as oil degraders was investigated in Sisal and Progreso, two port locations in the southeast Gulf of Mexico, both with a low level of hydrocarbon pollution. To do so, we determined the diversity and composition of bacterial communities in the marine sediment during the dry and rainy seasons using 16S rRNA sequencing. Functional profile analysis (PICRUTSt2) was used to predict metabolic functions associated with hydrocarbon degradation.

Results

We found a large bacterial taxonomic diversity, including some genera reported as hydrocarbon-degraders. Analyses of the alpha and beta diversity did not detect significant differences between sites or seasons, suggesting that location, season, and the contamination level detected here do not represent determining factors in the structure of the microbial communities. PICRUTSt2 predicted 10 metabolic functions associated with hydrocarbon degradation. Most bacterial genera with potential hydrocarbon bioremediation activity were generalists likely capable of degrading different hydrocarbon compounds. The bacterial composition and diversity reported here represent an initial attempt to characterize sites with low levels of contamination. This information is crucial for understanding the impact of eventual rises in hydrocarbon pollution.

The legacy of trace metal deposition from historical anthropogenic river management: A regional driver of offshore sedimentary microbial diversity

River management, both modern and historical, have dramatically modified offshore environments. While numerous studies have described the modern impacts, very few have evaluated the legacies remaining from hundreds of years ago. Herein, we show trace metal enrichment in the surface sediment of the abandoned Yellow River Delta, hypothesized to be associated with ancient river management. Essentially, anthropogenic modification caused the river to shift, creating a 12.4×10³ km² area with elevated trace metals; characterized by clear metal deposition gradients. Geographical factors related to the ancient river mouth had the most significant influences on Zn (explained by distance to the river mouth, DTM) and Cd (DTM and sediment salinity), while the sediment absorptive capacity was associated with the reallocation of Cu (clay, silt, and iron), Ni (clay and iron), and Pb (silt and iron). Trace metal legacies showed stronger influences on prokaryotic diversity than on micro-eukaryotic diversity, with the former best described by changes in rare, rather than dominant families and classes, and explainable by an "overlapping micro-niche" model. The ancient river's legacies provide evidence of longer-term human disturbance over hundreds of years; as its impacts on associated benthic microbiomes have led to lessons for modern-day waterway management of benthic ecosystems.

CeMbio - The Caenorhabditis elegans Microbiome Resource

The study of microbiomes by sequencing has revealed a plethora of correlations between microbial community composition and various life-history characteristics of the corresponding host species. However, inferring causation from correlation is often hampered by the sheer compositional complexity of microbiomes, even in simple organisms. Synthetic communities offer an effective approach to infer cause-effect relationships in host-microbiome systems. Yet the available communities suffer from several drawbacks, such as artificial (thus non-natural) choice of microbes, microbe-host mismatch (e.g., human microbes in gnotobiotic mice), or hosts lacking genetic tractability. Here we introduce CeMbio, a simplified natural Caenorhabditis elegans microbiota derived from our previous meta-analysis of the natural microbiome of this nematode. The CeMbio resource is amenable to all strengths of the C. elegans model system, strains included are readily culturable, they all colonize the worm gut individually, and comprise a robust community that distinctly affects nematode life-history. Several tools have additionally been developed for the CeMbio strains, including diagnostic PCR primers, completely sequenced genomes, and metabolic network models. With CeMbio, we provide a versatile resource and toolbox for the in-depth dissection of naturally relevant host-microbiome interactions in C. elegans.

Atrazine Removal from Municipal Wastewater Using a Membrane Bioreactor

As the demand for potable water increases, direct potable reuse of wastewater is an attractive alternative method to produce potable water. However, implementation of such a process will require the removal of emerging contaminants which could accumulate in the drinking water supply. Here, the removal of atrazine, a commonly used herbicide, has been investigated. Using real and synthetic wastewater, as well as sludge from two wastewater treatment facilities in the United States in Norman, Oklahoma and Fayetteville, Arkansas, atrazine removal has been investigated. Our results indicate that about 20% of the atrazine is removed by adsorption onto the particulate matter present. Significant biodegradation of atrazine was only observed under aerobic conditions for sludge from Norman, Oklahoma. Next-generation sequencing of the activated sludge revealed the abundance of Noncardiac with known atrazine degradation pathways in the Norman aerobic sludge, which is believed to be responsible for atrazine biodegradation in our study. The detection of these bacteria could also be used to determine the likelihood of biodegradation of atrazine for a given wastewater treatment facility.