Shifts In Bacterial Community Composition Research Articles

3D intrusions transport active surface microbial assemblages to the dark ocean

Subtropical oceans contribute significantly to global primary production, but the fate of the picophytoplankton that dominate in these low-nutrient regions is poorly understood. Working in the subtropical Mediterranean, we demonstrate that subduction of water at ocean fronts generates 3D intrusions with uncharacteristically high carbon, chlorophyll, and oxygen that extend below the sunlit photic zone into the dark ocean. These contain fresh picophytoplankton assemblages that resemble the photic-zone regions where the water originated. Intrusions propagate depth-dependent seasonal variations in microbial assemblages into the ocean interior. Strikingly, the intrusions included dominant biomass contributions from nonphotosynthetic bacteria and enrichment of enigmatic heterotrophic bacterial lineages. Thus, the intrusions not only deliver material that differs in composition and nutritional character from sinking detrital particles, but also drive shifts in bacterial community composition, organic matter processing, and interactions between surface and deep communities. Modeling efforts paired with global observations demonstrate that subduction can flux similar magnitudes of particulate organic carbon as sinking export, but is not accounted for in current export estimates and carbon cycle models. Intrusions formed by subduction are a particularly important mechanism for enhancing connectivity between surface and upper mesopelagic ecosystems in stratified subtropical ocean environments that are expanding due to the warming climate.

Biological and Synthetic Surfactants Increase Class I Integron Prevalence in Ex Situ Biofilms.

The role of biocides in the spread of antimicrobial resistance (AMR) has been addressed but only a few studies focus on the impact of surfactants on microbial diversity and AMR, although they are common constituents of cleaners, disinfectants, and personal care products and are thus released into the environment in large quantities. In this study, we used a static ex situ biofilm model to examine the development of four biofilms exposed to surfactants and analyzed the biofilms for their prevalence of class I integrons as a proxy for the overall abundance of AMR in a sample. We furthermore determined the shift in bacterial community composition by high-resolution melt analysis and 16S ribosomal RNA (16S rRNA) gene sequencing. Depending on the initial intrinsic prevalence of class I integrons in the respective ex situ biofilm, benzalkonium chloride, alkylbenzene sulfonate, and cocamidopropyl betaine increased its prevalence by up to 6.5× on average. For fatty alcohol ethoxylate and the biosurfactants sophorolipid and rhamnolipid, the mean increase did not exceed 2.5-fold. Across all surfactants, the increase in class I integrons was accompanied by a shift in bacterial community composition. Especially benzalkonium chloride, cocamidopropyl betaine, and alkylbenzene sulfonate changed the communities, while fatty alcohol ethoxylate, sophorolipid, and rhamnolipid had a lower effect on the bacterial biofilm composition.

Potential contributions of keystone species to intestinal ecosystem in patients with Crohn's disease.

Ravelling the central but poorly understood issue that potential contributions of keystone species to intestinal ecosystem functioning of patients with certain life-altering diseases including Crohn's disease (CD). In this study, a combination of 16S rRNA gene amplicon sequencing and amplicon-oriented metagenomic profiling was applied to gain insights into the shifts in bacterial community composition at different stages of CD course, and explore the functional roles of identified keystone species in intestinal microecosystem. Our results showed significant alterations in structure and composition of gut microbiota between CD patients and healthy control (HC) (P<0.05), but was no difference at active and remission stages. Whole-community-based comprehensive analyses were employed to identify the differential species such as Escherichia coli, Anaerostipes hadrus, and Eubacterium hallii in CD patients, with healthy populations as the control. Metagenome-wide functional analyses further revealed that the relative abundance of specialized metabolism-related genes such as cynS, frdB, serA, and gltB from these bacterial species in CD group was significantly different (P<0.05) from that in HC, and highlighted the potential roles of the keystone species in regulating the accumulation of important metabolites such as succinate, formate, ammonia, L-glutamate, and L-serine, which might have an effect on homeostasis of intestinal ecosystem. The findings identify several potential keystone species that may influence the intestinal microecosystem functioning of CD patients and provide some reference for future CD treatment.

Increased abundance of potentially pathogenic Vibrio and a marine heatwave co-occur with a Pacific Oyster summer mortality event

The Pacific Oyster (Crassostrea gigas) is an important aquaculture species, that has been globally affected by “summer mortality” outbreaks. The causes of summer mortality are often unclear, but several contributing factors have been implicated. To better understand the factors contributing to C. gigas summer mortality, we performed a 24 week experiment in tanks filled by a continuous flow of unfiltered surface seawater during a summer mortality high-risk period. Throughout this period, we measured a suite of environmental parameters, with weekly sampling to characterise the bacterial community composition, the abundance and diversity of the Vibrio genus, and the expression of oyster immune response genes. We observed three clear phases of oyster mortality: Phase 1 (day 0 to 75) was characterised by sporadic and low levels (mean < 1% per week) of oyster mortality; Phase 2 (day 82 to 119) involved constant levels of ongoing mortality (mean < 10% per week); and Phase 3 (day 125 to 161) involved a sharp increase in mortality (mean > 10% per week) reaching up to weekly mortality of 51%. The shift between phase 2 and 3 coincided with heavy rainfall and a marine heatwave (MHW) event at our study site, which lasted 13 days, when the average water temperature was elevated by 0.8 °C when compared to the weeks prior and following the MHW, and a maximum water temperature of 27.7 °C was reached. Oyster mortality was positively correlated with the occurrence of the MHW as well as bacterial and Vibrio abundance, and negatively correlated with seawater salinity that decreased from a salinity of 34.6 to 31.4 psu following rainfall events. In addition, the relative abundance of several Vibrio species, including V. campbellii, V. rotiferianus and V. owensii displayed positive correlations to oyster mortality. Shifts in the oyster-associated bacterial community and oyster immunity gene expression profiles occurred in parallel to increased mortality levels, with genes involved in the regulation of antimicrobial peptides (IkB1 and NF-kB p105) significantly over-expressed during high mortality. Overall, we observed a C. gigas mortality event that coincided with a marine heatwave, rainfall event and a shift in bacterial community composition. Our analyses provides further evidence for the putative role of Vibrio in summer mortality events.

Accumulation of polyethylene microplastics in river biofilms and effect on the uptake, biotransformation and toxicity of the antimicrobial triclosan

The interaction of multiple stressors in freshwater ecosystems may lead to adverse effects on aquatic communities and their ecological functions. Microplastics (MPs) are a class of contaminants of emerging concern that can exert both direct and indirect ecotoxicological effects. A growing number of studies have investigated MPs-attached microbial communities, but the interaction between MPs and substrate-associated biofilm (i.e., on natural river substrates, such as stones and sediments) remains poorly studied. In this work, the combined effects of polyethylene MPs (PE-MPs) with a particle size of 10–45 μm (2 mg/L) and the antimicrobial triclosan (TCS) (20 μg/L) were investigated on river biofilms through a short-term exposure experiment (72 h). To the best of authors’ knowledge, this is the first time that the combined effects of MPs and chemical contaminants in substrate-associated river biofilms were assessed. Different response parameters were evaluated, including (i) exposure assessment and ii) contaminants effects at different levels: bacterial community composition, antibiotic resistance, extracellular polymeric substances (EPS), photosynthetic efficiency (Yeff), and leucine aminopeptidase activity (LAPA). Triclosan was accumulated in river biofilms (1189–1513 ng/g dw) alongside its biotransformation product methyl-triclosan (20−29 ng/g dw). Also, PE-MPs were detected on biofilms (168−292 MP/cm2), but they had no significant influence on the bioaccumulation and biotransformation of TCS. A moderate shift in bacterial community composition was driven by TCS, regardless of PE-MPs co-exposure (e.g., increased relative abundance of Sphingomonadaceae family). Additionally, Yeff and EPS content were significantly disrupted in TCS-exposed biofilms. Therefore, the most remarkable effects on river biofilms were related to the antimicrobial TCS, whereas single PE-MPs exposure did not alter any of the evaluated parameters. These results demonstrate that biofilms might act as environmental sink of MPs. Although no interaction between PE-MPs and TCS was observed, the possible indirect impact of other MPs-adsorbed contaminants on biofilms should be further assessed.

Biogeographic Distribution of Soil Bacteria across Precipitation Gradient in Soil Profiles

The biogeographical distribution of soil microbial diversity, driven by climate change, notably precipitation, significantly influences soil functioning in diverse ecosystems. Land-use changes can alter ecosystem services mediated by microbial diversity, particularly in near-surface soil. In this study, we investigated soil bacterial diversity across precipitation gradients in various land uses. We focused on two soil layers (10-20 cm and 40-50 cm) in seven sampling areas along the Northeast China Transect. Utilizing 16S rRNA sequencing, we obtained 897,776,803 optimized sequences. The results reveal a significant shift in bacterial community composition with changing precipitation levels. As precipitation increases, the shifts in dominant bacterial phyla were generally observed. Additionally, soil depth played a role in structuring bacterial communities, with variations observed between surface and subsurface layers. Dominant taxa (Proteobacteria, Acidobacteria, Actinobacteria, Cholloroflexi) exhibited changes in the 10-20 cm layer due to human activity's influence, while the 40-50 cm layer showed more similarity, unaffected by human activities. Notably, parent material significantly affected soil bacterial diversity patterns, underscored by distinct habitats. Such results offer insights into climate change effects and parent material influences on soil bacterial diversity, highlighting the intricate interplay between precipitation, soil depth, and bacterial distribution; enhancing our understanding of ecosystem functioning and responses to environmental changes. This study contributes to the broader comprehension of microbial ecology and underscores the importance of considering multiple factors when studying soil bacterial dynamics.

Seasonal shifts in community composition and proteome expression in a sulphur-cycling cyanobacterial mat.

Seasonal changes in light and physicochemical conditions have strong impacts on cyanobacteria, but how they affect community structure, metabolism, and biogeochemistry of cyanobacterial mats remains unclear. Light may be particularly influential for cyanobacterial mats exposed to sulphide by altering the balance of oxygenic photosynthesis and sulphide-driven anoxygenic photosynthesis. We studied temporal shifts in irradiance, water chemistry, and community structure and function of microbial mats in the Middle Island Sinkhole (MIS), where anoxic and sulphate-rich groundwater provides habitat for cyanobacteria that conduct both oxygenic and anoxygenic photosynthesis. Seasonal changes in light and groundwater chemistry were accompanied by shifts in bacterial community composition, with a succession of dominant cyanobacteria from Phormidium to Planktothrix, and an increase in diatoms, sulphur-oxidizing bacteria, and sulphate-reducing bacteria from summer to autumn. Differential abundance of cyanobacterial light-harvesting proteins likely reflects a physiological response of cyanobacteria to light level. Beggiatoa sulphur oxidation proteins were more abundant in autumn. Correlated abundances of taxa through time suggest interactions between sulphur oxidizers and sulphate reducers, sulphate reducers and heterotrophs, and cyanobacteria and heterotrophs. These results support the conclusion that seasonal change, including light availability, has a strong influence on community composition and biogeochemical cycling of sulphur and O2 in cyanobacterial mats.

Effect of PVC microplastics on soil microbial community and nitrogen availability under laboratory-controlled and field-relevant temperatures

Microplastics have been reported to affect soil microbiota and nitrogen cycling under controlled temperature conditions, but their impact under field temperature regimes remains unclear. In this study, we compared the impacts of plasticized polyvinyl chloride (PVC) microplastics in an acidic agricultural soil at laboratory-controlled (25 °C) and field-relevant (outdoor ambient, 2–26 °C) temperature conditions. The results showed that changes in soil indicators were roughly the same under the two temperature conditions after 30 d, with increased NH4+-N content and urease activity, decreased NO3−-N content, potential nitrification rate and ammonia-oxidizing archaea abundance, unaltered bacterial abundance, and significant shifts in bacterial community composition. Probably because microbial activity differed at different temperatures, clear discrepancies were also observed: 1) the lowest observed effect concentration was 0.1 % w/w at 25 °C while it was 0.05 % w/w at ambient temperature; 2) a clear dose-effect relationship was observed at 25 °C but not at ambient temperature; and 3) in addition to a range of bacterial taxa that were commonly influenced by microplastics (e.g., Bradyrhizobium, Burkholderia-Caballeronia-Paraburkholderia, Sinomonas, and Sphingomonas), Amycolatopsis, Nocardia and unclassified Saccharimonadales were more responsive at 25 °C while Bacillus and Mycobacterium for ambient temperature. The findings provide insights into the interaction of microplastics with soil microbes under different temperatures and help to understand the threshold values of plasticized PVC microplastics in soil ecosystems.

Comparative study of bacterial community dynamics in different soils following application of the herbicide atrazine

Microbial communities in cultivated soils control the fate of pollutants associated with agricultural practice. The present study was designed to explore the response of bacterial communities to the application of the widely-used herbicide atrazine in three different crop fields that differ significantly in their physicochemical structure and nutritional content: the nutrient-rich (with relatively high carbon and nitrogen content) Newe Yaar (NY) and Ha-Ogen (HO) soils and the nutrient-poor, sandy Sde-Eliyahu (SE) soil. The 16 S rRNA gene amplicon sequencing revealed the nutrient poor HO soil differs in its response to atrazine in comparison to the two nutrient-rich soils both in the shortest persistence of atrazine and its effect on community structure and composition. Potential reported bacterial degraders of atrazine such as Pseudomonas, Clostridium and Bacillus were more abundant in contaminated sandy/poor soils (HO) whereas bacteria known for nitrogen cycling such as Azospirillum, Sinorhizobium, Nitrospira and Azohydromonas were significantly more abundant in the nutrient rich contaminated SE soils. No significant increase of potential indigenous degrader Arthrobacter was detected in SE and NY soils whereas a significant increase was recorded with HO soils. An overall shift in bacterial community composition following atrazine application was observed only in the nutrient poor soil. Understanding atrazine persistence and microbiome response to its application of in dependence with soil types serve the design of precision application strategies.

Urbanization Imprint on Soil Bacterial Communities in Forests and Grasslands

Urbanization alters land uses and creates heterogeneous environmental conditions in cities and their surroundings, which may directly or indirectly impact soil microorganisms. However, how urbanization affects soil bacterial diversity and community composition, particularly in different land use types, remains largely unknown. In this study, we collected 36 soil samples (18 forest and 18 grass soils) along a rural-suburban-urban gradient in Chang-Zhu-Tan agglomeration. The bacterial diversity and community composition were investigated using 16S rRNA gene sequencing that targeted the V3-V4 region. Our results showed that urbanization induced shifts in bacterial diversity and community composition in both forestlands and grasslands. Specifically, soil bacterial diversity was higher in urban areas than in their suburban and rural counterparts in forests and grasslands, particularly in forests, where significant increases were detected. Urbanization changed the most dominated soil bacterial community from Acidobacteria to Proteobacteria in forestland. Significant decrease and increase were observed in the relative abundance of Acidobacteria (e.g., Acidobacteriales, Acidobacteriia_Subgroup2 and Solibacterales) and Proteobacteria (e.g., Betaproteobacteriales, Myxococcales and Sphingomonadales), respectively, in the forests with increasing urbanization intensity. In contrast, Proteobacteria always dominated the soil bacterial community along the rural-suburban-urban gradient in grassland, and significant decrease and increase in Nitrospirae and Latescibacteria were induced by urbanization, respectively. In addition to urbanization and total nitrogen, total organic carbon and ratio of carbon and nitrogen were the main factors that related with the bacterial community in forest soils, whereas soil water content was the main factor related with soil bacterial community in the grasslands. Together, our results indicate that the urbanization results in shifts in bacterial community composition and diversity, but the extent varied between forest and grassland, which may due to different human management intensity.

Distinct roles of bacteria and fungi in mediating soil extracellular enzymes under long-term nitrogen deposition in temperate plantations

Soil microbes decompose soil organic matter by producing various extracellular enzymes, and also regulate soil carbon (C) and nutrient cycles. However, how shifts in soil microbial community under long-term nitrogen (N) deposition govern soil extracellular enzyme activities (EEAs) is not known. Here, we conducted a decade-long N fertilization experiment consisting of control, low-N (2 g N m−2 year−1), medium-N (5 g N m−2 year−1), and high-N (10 g N m−2 year−1) treatments in a N-limited temperate plantation in northern China. The diversity and community composition of fungi and bacteria were determined with bacterial 16S rRNA genes and fungal internal transcribed spacer genes sequencing. Soil EEAs involved in C, N, and phosphorus (P) cycles were also measured. The results showed that high-N addition increased fungal diversity and altered microbial community composition. In particular, rare fungal diversity and rare bacterial community composition were more sensitive to N addition. N addition improved β-1,4-glucosidase (BG) and acid phosphatase (AP) activities by altering bacterial community composition, and inhibited leucine aminopeptidase (LAP) and polyphenolic oxidase (PPO) activities by affecting fungal functional groups. Specifically, shifts in bacterial community composition caused by N addition were reflected in the significant increase in the dominant class Thermoleophilia, which could be an indicator of secreted hydrolase involved in C and P cycles. Symbiotrophic fungi were more closely associated with LAP for acquiring N and PPO. Our data provide a novel view of the link between major extracellular enzymes and specific microbial taxa under the background of N deposition.

Intestinal Microbiome Richness of Coral Reef Damselfishes (Actinopterygii: Pomacentridae).

Fish gastro-intestinal system harbors diverse microbiomes that affect the host's digestion, nutrition, and immunity. Despite the great taxonomic diversity of fish, little is understood about fish microbiome and the factors that determine its structure and composition. Damselfish are important coral reef species that play pivotal roles in determining algae and coral population structures of reefs. Broadly, damselfish belong to either of two trophic guilds based on whether they are planktivorous or algae-farming. In this study, we used 16S rRNA gene sequencing to investigate the intestinal microbiome of 5 planktivorous and 5 algae-farming damselfish species (Pomacentridae) from the Great Barrier Reef. We detected Gammaproteobacteria ASVs belonging to the genus Actinobacillus in 80% of sampled individuals across the 2 trophic guilds, thus, bacteria in this genus can be considered possible core members of pomacentrid microbiomes. Algae-farming damselfish had greater bacterial alpha-diversity, a more diverse core microbiome and shared 35 ± 22 ASVs, whereas planktivorous species shared 7 ± 3 ASVs. Our data also highlight differences in microbiomes associated with both trophic guilds. For instance, algae-farming damselfish were enriched in Pasteurellaceae, whilst planktivorous damselfish in Vibrionaceae. Finally, we show shifts in bacterial community composition along the intestines. ASVs associated with the classes Bacteroidia, Clostridia, and Mollicutes bacteria were predominant in the anterior intestinal regions while Gammaproteobacteria abundance was higher in the stomach. Our results suggest that the richness of the intestinal bacterial communities of damselfish reflects host species diet and trophic guild.

Optimal growth temperature of Arctic soil bacterial communities increases under experimental warming.

Future climate warming in the Arctic will likely increase the vulnerability of soil carbon stocks to microbial decomposition. However, it remains uncertain to what extent decomposition rates will change in a warmer Arctic, because extended soil warming could induce temperature adaptation of bacterial communities. Here we show that experimental warming induces shifts in the temperature–growth relationships of bacterial communities, which is driven by community turnover and is common across a diverse set of 8 (sub) Arctic soils. The optimal growth temperature (T opt) of the soil bacterial communities increased 0.27 ± 0.039 (SE) and 0.07 ± 0.028°C per °C of warming over a 0–30°C gradient, depending on the sampling moment. We identify a potential role for substrate depletion and time‐lag effects as drivers of temperature adaption in soil bacterial communities, which possibly explain discrepancies between earlier incubation and field studies. The changes in T opt were accompanied by species‐level shifts in bacterial community composition, which were mostly soil specific. Despite the clear physiological responses to warming, there was no evidence for a common set of temperature‐responsive bacterial amplicon sequence variants. This implies that community composition data without accompanying physiological measurements may have limited utility for the identification of (potential) temperature adaption of soil bacterial communities in the Arctic. Since bacterial communities in Arctic soils are likely to adapt to increasing soil temperature under future climate change, this adaptation to higher temperature should be implemented in soil organic carbon modeling for accurate predictions of the dynamics of Arctic soil carbon stocks.

Nitrogen Enrichment Reduces the Diversity of Bacteria and Alters Their Nutrient Strategies in Intertidal Zones

Intertidal ecosystems are affected by severe nitrogen (N) pollution as a result of anthropogenic activities, and it is unclear how this may affect intertidal microbial communities, which play critical roles in regulating biogeochemical cycles. To address this gap, we conducted a two-month mesocosm experiment using six targeted concentrations of total N. The findings indicated that N entering seawaters has direct negative effects on the bacterial diversity. Dose dependence was found for the effects of N on bacterial diversity in sediment: low N addition increased the bacterial diversity, but a reduction in bacterial diversity occurred when N exceeded a certain value (≥ 3 mg L−1). Additionally, N enrichment caused clear shifts in bacterial community composition with increases in the relative abundance of Balneola (organic-degrading), Phalacroma mitra (carbohydrate-fermenting), and Bacteroides (phosphorus (P)-solubilizing), and decreases in Leptolyngbya_PPC_6406 (N2-fixing). The increased abundance in P-solubilizing and organic-degrading bacteria and decrease in N-fixing bacteria, combined with the upregulated activity of alkaline phosphatase and downregulation of urease activity, implied that the bacterial assemblage tended to be more effective in P and carbon acquisition but reduced N acquisition. Further path analysis suggested that N had direct effects on bacteria and contributed 50%–100% to the variations in bacterial diversity, whereas environmental changes such as dissolved oxygen and pH played minor roles. Overall, bacteria occurring in sediment were likely more stress-resistant to high N exposure than those occurring in seawater, possibly due to the high buffering capacity of sediment and growth tolerances of bacteria in the sediment. These findings point to the vulnerability of microbes in water systems to increasing global N loading, and that N reduction is needed to combat the loss of microbial diversity.

Rhizosphere and Straw Return Interactively Shape Rhizosphere Bacterial Community Composition and Nitrogen Cycling in Paddy Soil.

Currently, how rice roots interact with straw return in structuring rhizosphere communities and nitrogen (N) cycling functions is relatively unexplored. In this study, paddy soil was amended with wheat straw at 1 and 2% w/w and used for rice growth. The effects of the rhizosphere, straw, and their interaction on soil bacterial community composition and N-cycling gene abundances were assessed at the rice maturity stage. For the soil without straw addition, rice growth, i.e., the rhizosphere effect, significantly altered the bacterial community composition and abundances of N-cycling genes, such as archaeal and bacterial amoA (AOA and AOB), nirK, and nosZ. The comparison of bulk soils between control and straw treatments showed a shift in bacterial community composition and decreased abundance of AOA, AOB, nirS, and nosZ, which were attributed to sole straw effects. The comparison of rhizosphere soils between control and straw treatments showed an increase in the nifH gene and a decrease in the nirK gene, which were attributed to the interaction of straw and the rhizosphere. The number of differentially abundant genera in bulk soils between control and straw treatments was 13–23, similar to the number of 16–22 genera in rhizosphere soil between control and straw treatment. However, the number of genera affected by the rhizosphere effect was much lower in soil amended with straw (3–4) than in soil without straw addition (9). Results suggest possibly more pronounced impacts of straw amendments in shaping soil bacterial community composition.

A pilot study demonstrating the impact of surgical bowel preparation on intestinal microbiota composition following colon and rectal surgery

The intestinal microbiota has been implicated in the pathogenesis of complications following colorectal surgery, yet perioperative changes in gut microbiome composition are poorly understood. The objective of this study was to characterize the perioperative gut microbiome in patients undergoing colonoscopy and colorectal surgery and determine factors influencing its composition. Using Illumina amplicon sequencing coupled with targeted metabolomics, we characterized the fecal microbiota in: (A) patients (n = 15) undergoing colonoscopy who received mechanical bowel preparation, and (B) patients (n = 15) undergoing colorectal surgery who received surgical bowel preparation, composed of mechanical bowel preparation with oral antibiotics, and perioperative intravenous antibiotics. Microbiome composition was characterized before and up to six months following each intervention. Colonoscopy patients had minor shifts in bacterial community composition that recovered to baseline at a mean of 3 (1–13) days. Surgery patients demonstrated substantial shifts in bacterial composition with greater abundances of Enterococcus, Lactobacillus, and Streptococcus. Compositional changes persisted in the early postoperative period with recovery to baseline beginning at a mean of 31 (16–43) days. Our results support surgical bowel preparation as a factor significantly influencing gut microbial composition following colorectal surgery, while mechanical bowel preparation has little impact.

Near-universal trends in brGDGT lipid distributions in nature.

Bacterial brGDGT lipids are a prevalent tool in studies of terrestrial paleoclimate. Their distributions correlate empirically with environmental temperature and pH, and their ubiquity in terrestrial, freshwater, and marine environments gives them wide applicability. Whether correlations with temperature and pH emerge due to a physiological response of source organisms and/or a shift in bacterial community composition remains an open question with important implications for proxy development and application. We applied a newly described technique for grouping brGDGTs to a globally compiled dataset (n = 3129) consisting of all modern sample media known to host brGDGTs. We found strong resemblances in the relationships between brGDGT fractional abundances and both temperature and pH across nearly all sample types examined. We also found near-universal connections between the brGDGTs themselves. Given the markedly different bacterial communities expected to inhabit these settings, these widespread relationships may suggest physiological and/or biochemical bases for observed brGDGT distributions.

Bacterioplankton Community Profiling of the Surface Waters of Kuwait

The marine waters of Kuwait are highly dynamic and strongly influenced by extreme environmental conditions and high levels of anthropogenic activities. This study explored the bacterioplankton community composition and diversity in Kuwait Bay and at four offshore sites close to urbanized coastal areas during two seasons, autumn (October) and spring (April). 16S rRNA amplicon sequencing detected higher bacterial diversity and richness in spring than in autumn. Also, bacterial community beta diversity revealed a significant seasonal partitioning between the two sampling periods but no clear spatial variation could be depicted. Alphaproteobacteria, Gammaproteobacteria, Cyanobacteria, Flavobacteriia, and Acidimicrobiia dominated the seasonal samples, and SARII clade Ia, SARII clade II, Synechococcus, and SUP05 cluster were among the most abundant taxa in the seasonal samples. However, the strong temporal shift in bacterial community composition was related to Synechococcus abundance. The prevailing physicochemical parameters displayed a significant influence on the bacterioplankton community composition, which was mainly driven by shifts in temperature and nutrient inputs. Furthermore, functional prediction by PICRUSt analysis revealed a relatively stable conserved functional profile in Kuwait’s waters. However, functional genes related to membrane transport were enriched in eutrophic spring waters, while photosynthetic genes were enriched in autumn. Our results provide in-depth insights into the temporal and spatial variations of bacterioplankton dynamics in Kuwait waters and highlight the strong seasonal influence of natural and anthropogenic stressors on their composition and predicted functional capabilities.

Microbial Community Composition and Activity in Saline Soils of Coastal Agro-Ecosystems.

Soil salinity is a serious problem for agriculture in coastal regions. Nevertheless, the effects of soil salinity on microbial community composition and their metabolic activities are far from clear. To improve such understanding, we studied microbial diversity, community composition, and potential metabolic activity of agricultural soils covering non–, mild–, and severe–salinity. The results showed that salinity had no significant effect on bacterial richness; however, it was the major driver of a shift in bacterial community composition and it significantly reduced microbial activity. Abundant and diverse of microbial communities were detected in the severe–salinity soils with an enriched population of salt–tolerant species. Co–occurrence network analysis revealed stronger dependencies between species associated with severe salinity soils. Results of microcalorimetric technology indicated that, after glucose amendment, there was no significant difference in microbial potential activity among soils with the three salinity levels. Although the salt prolonged the lag time of microbial communities, the activated microorganisms had a higher growth rate. In conclusion, salinity shapes soil microbial community composition and reduces microbial activity. An addition of labile organic amendments can greatly alleviate salt restrictions on microbial activity, which provides new insight for enhancing microbial ecological functions in salt–affected soils.

Tap water as a natural vehicle for microorganisms shaping the human gut microbiome.

Fresh potable water is an indispensable drink which humans consume daily in substantial amounts. Nonetheless, very little is known about the composition of the microbial community inhabiting drinking water or its impact on our gut microbiota. In the current study, an exhaustive shotgun metagenomics analysis of the tap water microbiome highlighted the occurrence of a highly genetic biodiversity of the microbial communities residing in fresh water and the existence of a conserved core tap water microbiota largely represented by novel microbial species, representing microbial dark matter. Furthermore, genome reconstruction of this microbial dark matter from water samples unveiled homologous sequences present in the faecal microbiome of humans from various geographical locations. Accordingly, investigation of the faecal microbiota content of a subject that daily consumed tap water for 3 years provides proof for horizontal transmission and colonization of water bacteria in the human gut.