Total Microbial Community Research Articles

The different responses of planktonic bacteria and archaea to water temperature maintain the stability of their community diversity in dammed rivers

BackgroundPlanktonic bacteria and archaea play a key role in river nutrient biogeochemical cycling; however, their respective community assembly and how to maintain their diversity are not well known in dammed rivers. Therefore, a seasonal survey of planktonic bacterial and archaeal community compositions and related environmental factors was conducted in 16 cascade reservoirs and corresponding river waters on the Wujiang River and the Pearl River in southwest China to understand the above mechanisms.ResultsDeterministic processes dominated bacterial and archaeal community assembly. The structural equation models showed that water temperature can directly or indirectly affect the microbial diversity. Interestingly, planktonic bacterial diversity increased with increasing water temperature, while archaea showed the opposite trend; the overall diversity of bacteria and archaea was no significant changes with changeable water temperature. Abundant microbes had a stronger distance–decay relationship than middle and rare ones, and the relationship was stronger in winter and spring than in summer and autumn.ConclusionsPlanktonic bacteria and archaea in dammed rivers had different biogeographic distributions, and water temperature was a key controlling factor. The different responses of planktonic bacterial and archaeal diversity to water temperature could be due to their different phylogenetic diversity. This ultimately maintained the stability of total microbial community diversity. This study reveals the different responses of planktonic bacteria and archaea to water temperature and perfects the theoretical framework for planktonic microbial biogeography in dammed rivers.

Enrichment of rare methanogenic Archaea shows their important ecological role in natural high-CO2 terrestrial subsurface environments.

Long-term stability of underground CO2 storage is partially affected by microbial activity but our knowledge of these effects is limited, mainly due to a lack of sites. A consistently high flux of mantle-derived CO2 makes the Eger Rift in the Czech Republic a natural analogue to underground CO2 storage. The Eger Rift is a seismically active region and H2 is produced abiotically during earthquakes, providing energy to indigenous microbial communities. To investigate the response of a microbial ecosystem to high levels of CO2 and H2, we enriched microorganisms from samples from a 239.5 m long drill core from the Eger Rift. Microbial abundance, diversity and community structure were assessed using qPCR and 16S rRNA gene sequencing. Enrichment cultures were set up with minimal mineral media and H2/CO2 headspace to simulate a seismically active period with elevated H2. Methane headspace concentrations in the enrichments indicated that active methanogens were almost exclusively restricted to enrichment cultures from Miocene lacustrine deposits (50-60 m), for which we observed the most significant growth. Taxonomic assessment showed microbial communities in these enrichments to be less diverse than those with little or no growth. Active enrichments were especially abundant in methanogens of the taxa Methanobacterium and Methanosphaerula. Concurrent to the emergence of methanogenic archaea, we also observed sulfate reducers with the metabolic ability to utilize H2 and CO2, specifically the genus Desulfosporosinus, which were able to outcompete methanogens in several enrichments. Low microbial abundance and a diverse non-CO2 driven microbial community, similar to that in drill core samples, also reflect the inactivity in these cultures. Significant growth of sulfate reducing and methanogenic microbial taxa, which make up only a small fraction of the total microbial community, emphasize the need to account for rare biosphere taxa when assessing the metabolic potential of microbial subsurface populations. The observation that CO2 and H2-utilizing microorganisms could only be enriched from a narrow depth interval suggests that factors such as sediment heterogeneity may also be important. This study provides new insight on subsurface microbes under the influence of high CO2 concentrations, similar to those found in CCS sites.

Distribution and survival strategies of endemic and cosmopolitan diazotrophs in the Arctic Ocean

Dinitrogen (N2) fixation is the major source of reactive nitrogen in the ocean and has been considered to occur specifically in low-latitude oligotrophic oceans. Recent studies have shown that N2 fixation also occurs in the polar regions and thus is a global process, although the physiological and ecological characteristics of polar diazotrophs are not yet known. Here, we successfully reconstructed diazotroph genomes, including that of cyanobacterium UCYN-A (Candidatus ‘Atelocyanobacterium thalassa’), from metagenome data corresponding to 111 samples isolated from the Arctic Ocean. These diazotrophs were highly abundant in the Arctic Ocean (max., 1.28% of the total microbial community), suggesting that they have important roles in the Arctic ecosystem and biogeochemical cycles. Further, we show that diazotrophs within genera Arcobacter, Psychromonas, and Oceanobacter are prevalent in the <0.2 µm fraction in the Arctic Ocean, indicating that current methods cannot capture their N2 fixation. Diazotrophs in the Arctic Ocean were either Arctic-endemic or cosmopolitan species from their global distribution patterns. Arctic-endemic diazotrophs, including Arctic UCYN-A, were similar to low-latitude-endemic and cosmopolitan diazotrophs in genome-wide function, however, they had unique gene sets (e.g., diverse aromatics degradation genes), suggesting adaptations to Arctic-specific conditions. Cosmopolitan diazotrophs were generally non-cyanobacteria and commonly had the gene that encodes the cold-inducible RNA chaperone, which presumably makes their survival possible even in deep, cold waters of global ocean and polar surface waters. This study shows global distribution pattern of diazotrophs with their genomes and provides clues to answering the question of how diazotrophs can inhabit polar waters.

Microbial community and antibiotic resistance gene distribution in food waste, anaerobic digestate, and paddy soil

The study assessed the occurrence and distribution of microbial community and antibiotic resistance genes (ARGs) in food waste, anaerobic digestate, and paddy soil samples, and revealed the potential hosts of ARGs and factors influencing their distribution. A total of 24 bacterial phyla were identified, of which 16 were shared by all samples, with Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria accounting for 65.9–92.3 % of the total bacterial community. Firmicutes was the most abundant bacteria in food waste and digestate samples, accounting for 33–83 % of the total microbial community. However, in paddy soil samples with digestate, Proteobacteria had the highest relative abundance of 38–60 %. Further, 22 ARGs were detected in food waste and digestate samples, with multidrug, macrolide-lincosamide-streptogramin (MLS), bacitracin, aminoglycoside, tetracycline, vancomycin, sulfonamide, and rifamycin resistance genes being the most abundant and shared by all samples. The highest total relative abundance of ARGs in food waste, digestate, and soil without and with digestate was detected in samples from January 2020, May 2020, October 2019, and May 2020, respectively. The MLS, vancomycin, tetracycline, aminoglycoside, and sulfonamide resistance genes had higher relative abundance in food waste and anaerobic digestate samples, whereas multidrug, bacteriocin, quinolone, and rifampin resistance genes were more abundant in paddy soil samples. Redundancy analysis demonstrated that aminoglycoside, tetracycline, sulfonamide, and rifamycin resistance genes were positively correlated with total ammonia nitrogen and pH of food waste and digestate samples. Vancomycin, multidrug, bacitracin, and fosmidomycin resistance genes had positive correlations with potassium, moisture, and organic matter in soil samples. The co-occurrence of ARG subtypes with bacterial genera was investigated using network analysis. Actinobacteria, Proteobacteria, Bacteroidetes, and Acidobacteria were identified as potential hosts of multidrug resistance genes.

Remediation of petroleum contaminated soil by persulfate oxidation coupled with microbial degradation

This study was conducted on soil polluted with high concentrations of crude oil (12,835 ± 572.76 mg/kg) with different dosages of persulfate (PS) coupled with hydrocarbon-degrading mixed bacteria (including Enterobacteriaceae, Stenotrophomonas, Pseudomonas, Acinetobacter, and Achromobacter) obtained from long-term oil-contaminated soil. The interaction among total petroleum hydrocarbons (TPH), soil parameters, and microbial communities during a 187-d combined remediation process was evaluated. The result showed that the TPH removal of 1% PS oxidation combined with bioremediation was 80.05%; this was 4.88% and 20.94% higher than that of bioremediation and 1% PS oxidation combined with natural attenuation. This is a result of 1%PS stimulated enzyme secretion and dissolved organic carbon content, especially fulvic acid, improving TPH mobility and bioavailability in soil. Furthermore, introducing mixed bacteria after oxidation further increased enzyme activities and TPH-degrading ability, thus promoting carbon substrate conversion and biodegradation rate. Conversely, the excessive oxidation of 3% and 5% PS had a negative impact on the soil environment and microbial diversity resulting in lower TPH degradation (36%-57%). High-throughput sequencing revealed that the abundance and diversity of soil bacteria decreased in all remediation groups compared to those in the pristine soil. Redundancy analysis showed that the main factors affecting 1% PS oxidation combined with bioremediation during subsequent microbial remediation were pH, cation exchange capacity, and lipase activity, which may indirectly influence TPH biodegradation by increasing the abundance of genus Immundisolibacteraceae, Comamonadaceae, and Acinetobacter. This study provides data on in situ chemical oxidation integrated with the bioremediation of petroleum hydrocarbon-contaminated soils.

Response of soil microbial Communities, inorganic and organic soil carbon pools in arid saline soils to alternative land use practices

Soil organic and inorganic carbon (SOC & SIC) and microbial community structure are key indicators of soil quality and productivity in arid-saline soils. Salinity stress and diminishing availability of freshwater (FW) for irrigation are major constraints for productivity and improving soil quality indicators. Using treated wastewater (TW) and implementing climate-smart cropping systems are promising alternatives to replace freshwater usage in intensive cropping systems, however, impacts on the microbial community and net-carbon sequestration potential are not clearly understood. This field study was conducted in an arid saline-soil to investigate soil microbial community structure and soil carbon contents under a combination of treatments comparing bioenergy sorghum (So) and switchgrass (Sg), two irrigation water sources (FW & TW), and gypsum amendment (GA), to a native-soil control. After three years of implementing these treatments, soil samples were collected and analyzed for total carbon (TC), SOC, SIC, microbial biomass-carbon (MBC) and microbial community structure. Results showed that TW increased microbial diversity and shifted the community structure towards copiotroph-dominated prokaryotes. Several predominant and responsive taxa were associated with divergent trends of SOC, SIC and salinity parameters. Both SOC and SIC pools were sensitive to treatments and demonstrated divergent trends, as contents of TC and SOC were higher in TW-treatments, but of SIC were significantly lower in several So_TW treatments. Treatment TW_So_GA assembled a distinctive microbial community structure, accumulated the highest content of SOC (7.66 g kg−1) but recorded the lowest content of SIC (6.63 g kg−1). The lowest content of SOC was observed in native soil (4.58 g kg−1) but contained the highest SIC (8.15 g kg−1). The study results revealed the agronomic systems with higher potential for increasing TC and SOC content in arid-saline soils. Surface soil SIC was responsive to agronomic management, and several treatments produced disparate impacts on SOC and SIC stocks, which warrant for considering TC as the key indicator for assessing carbon sequestration in arid lands.

Biogeographic distribution, ecotype partitioning and controlling factors of Chloroflexi in the sediments of six hadal trenches of the Pacific Ocean

The hadal trenches are “hot spots” for mineralization of organic matter in the deep ocean. Chloroflexi are one of the most dominant and active taxa in trench sediments, serving as important drivers of carbon cycles in hadal trenches. However, current understanding on hadal Chloroflexi is largely restricted to individual trench. This study systematically analyzed the diversity, biogeographic distribution, ecotype partitioning as well as environmental drivers of Chloroflexi in the sediments of hadal trenches, by reanalyzing 16S rRNA gene libraries of 372 samples from 6 trenches around the Pacific Ocean. The results showed that Chloroflexi averagely account for 10.10 % and up to 59.95 % of total microbial communities in the trench sediments. Positive correlations between relative abundance of Chloroflexi and depths down the vertical sediment profiles were observed in all of the sediment cores analyzed, suggesting the increasing significance of Chloroflexi in deeper sediment layers. Overall, trench sediment Chloroflexi were mainly composed of the classes Dehalococcidia, Anaerolineae and JG30-KF-CM66, and four orders i.e. SAR202, Anaerolineales, norank JG30-KF-CM66 and S085, were identified as core taxa that were dominant and prevalent in the hadal trench sediments. A total of 22 subclusters were identified within these core orders, and distinct patterns of ecotype partitioning related with depths down the vertical sediment profiles were observed, suggesting the great diversification of metabolic potentials and environment preference of different Chloroflexi lineages. The spatial distribution of hadal Chloroflexi were found to be significantly related with multiple environmental factors, while depths down the vertical sediment profiles explained the highest proportion of variations. These results provide valuable information for further exploring the roles of Chloroflexi in biogeochemical cycle of the hadal zone, and lay the foundation for understanding the adaptive mechanisms and evolutionary characteristics of microorganisms in hadal trenches.

Comparative Study of Microbial Diversity in Different Coastal Aquifers: Determining Factors

Coastal aquifers have been extensively studied from the hydrodynamic and geochemical points of view, but there is still a significant gap in the knowledge of their microbial diversity. The bacterial communities of four coastal aquifers at different depths and salinities were studied in order to infer the anthropogenic and physico-chemical influences on groundwater microbiota. At the physico-chemical level, samples from different aquifers, but with similar salinities, are more similar than those taken within the same aquifer. The microbial community at the phylum level shows the dominance of Proteobacteria, Firmicutes, and Actinobacteria. Samples from the same aquifer, although having very different salinities, are more similar than samples with similar physico-chemical characteristics. Therefore, the taxa present in these media are resilient to environmental variations. The aquifer preserving the most pristine conditions harbors the lowest values of biodiversity, compared to those affected by anthropic activities. The incorporation of pollutants into the aquifer favors the development of a so-called “rare biosphere”, consisting of a high number of taxa which represent a low percentage (&lt;1%) of the total microbial community. The analysis of microbial biodiversity in a coastal aquifer could be used as an indicator of the degree of anthropic alteration.

Exploration of microbiome diversity of stacked fermented grains by flow cytometry and cell sorting.

Sauce-flavor baijiu is one of the twelve flavor types of Chinese distilled fermented product. Microbial composition plays a key role in the stacked fermentation of Baijiu, which uses grains as raw materials and produces flavor compounds, however, the active microbial community and its relationship remain unclear. Here, we investigated the total and active microbial communities of stacked fermented grains of sauce-flavored Baijiu using flow cytometry and high-throughput sequencing technology, respectively. By using traditional high-throughput sequencing technology, a total of 24 bacterial and 14 fungal genera were identified as the core microbiota, the core bacteria were Lactobacillus (0.08-39.05%), Acetobacter (0.25-81.92%), Weissella (0.03-29.61%), etc. The core fungi were Issatchenkia (23.11-98.21%), Monascus (0.02-26.36%), Pichia (0.33-37.56%), etc. In contrast, using flow cytometry combined with high-throughput sequencing, the active dominant bacterial genera after cell sorting were found to be Herbaspirillum, Chitinophaga, Ralstonia, Phenylobacterium, Mucilaginibacter, and Bradyrhizobium, etc., whereas the active dominant fungal genera detected were Aspergillus, Pichia, Exophiala, Candelabrochaete, Italiomyces, and Papiliotrema, etc. These results indicate that although the abundance of Acetobacter, Monascus, and Issatchenkia was high after stacked fermentation, they may have little biological activity. Flow cytometry and cell sorting techniques have been used in the study of beer and wine, but exploring the microbiome in such a complex environment as Chinese baijiu has not been reported. The results also reveal that flow cytometry and cell sorting are convenient methods for rapidly monitoring complex microbial flora and can assist in exploring complex environmental samples.

Combined effects of long-term tillage and fertilisation regimes on soil organic carbon, microbial biomass, and abundance of the total microbial communities and N-functional guilds

Reduced tillage intensity is known to increase soil organic carbon (SOC) in the topsoil, but can also lead to increased microbially derived nitrous oxide (N2O) emissions. Although the trade-offs between C sequestration and N2O emissions under different agricultural practices have been extensively investigated, the reported results are conflicting and, thus remain unclear. In this study, the effects of different types of tillage [no-till (NT) and conventional mouldboard tillage (CT)] in combination with four fertilisation regimes [unfertilised control (CON), mineral NPK (MIN), organic (compost) (ORG), and mixed (NPK + compost) (MIX)] on SOC and microbial biomass (Cmic) were examined two decades after the experiment was initiated. The abundance of the microbial community and N-functional guilds within the soil profile (up to a depth of 60 cm) was also determined. SOC content was significantly higher in NT than in CT at 0–10 cm depth, with an average difference of 0.6–1.3 % SOC, depending on fertilisation. Organic fertilisation increased the SOC content in both tillage systems up to a depth of 20 cm. Microbial biomass, abundance of total bacterial and archaeal 16S rRNA, and fungal ITS genes decreased with depth, corresponding to the decrease in SOC, and, consequently, were higher in NT than in CT, in the top 20 cm soil for microbial biomass and bacterial abundance and top 10 cm for fungi and archaea. Denitrifiers and ammonium oxidising archaea (AOA) were affected by soil depth and tillage, whereas the distribution of ammonium oxidising bacteria (AOB) was affected by fertilisation and depth. The ratios between (i) the two nitrite-reducing communities (nirS/nirK), (ii) the two N2O-reducing communities (nosZI/nosZII), and (iii) the nitrite- and N2O-reducing communities [(nirK + nirS)/(nosZ + nosZII)] increased significantly with soil depth, indicating niche differentiation caused by differences in nutrients contents and environmental conditions. Overall, stratification of SOC and nutrients in the soil by tillage and fertilisation was the main driver of the differences in the total microbial and N cycling communities. The findings of our study provide novel insights that can aid in development of effective strategies for steering soil microbiome responsible for N2O emissions.

Determinants of Total and Active Microbial Communities Associated with Cyanobacterial Aggregates in a Eutrophic Lake

Cyanobacterial aggregates (CAs) comprised of photosynthetic and phycospheric microorganisms are often the cause of cyanobacterial blooms in eutrophic freshwater lakes. Although phylogenetic diversity in CAs has been extensively studied, much less was understood about the activity status of microorganisms inside CAs and determinants of their activities. In this study, the 16S rRNA gene (rDNA)-based total communities within CAs in Lake Taihu of China were analyzed over a period of 6 months during the bloom season; the 16S rRNA-based active communities during daytime, nighttime, and under anoxic conditions were also profiled. Synchronous turnover of both cyanobacterial and phycospheric communities was observed, suggesting the presence of close interactions. The rRNA/rDNA ratio-based relative activities of individual taxa were predominantly determined by their rDNA-based relative abundances. In particular, high-abundance taxa demonstrated comparatively lower activities, whereas low-abundance taxa were generally more active. In comparison, hydrophysicochemical factors as well as diurnal and redox conditions showed much less impact on relative activities of microbial taxa within CAs. Nonetheless, total and active communities exhibited differences in community assembly processes, the former of which were almost exclusively controlled by homogeneous selection during daytime and under anoxia. Taken together, the results from this study provide novel insights into the relationships among microbial activities, community structure, and environmental conditions and highlight the importance of further exploring the regulatory mechanisms of microbial activities at the community level. IMPORTANCE Cyanobacterial aggregates are important mediators of biogeochemical cycles in eutrophic lakes during cyanobacterial blooms, yet regulators of microbial activities within them are not well understood. This study revealed rDNA-based abundances strongly affected the relative activities of microbial taxa within Microcystis aggregates, as well as trade-off effects between microbial abundances and activities. Environmental conditions further improved the levels of relative activities and affected community assembly mechanisms in phycospheric communities. The relationships among microbial activities, abundances, and environmental conditions improve our understanding of the regulatory mechanisms of microbial activities in cyanobacterial aggregates and also provide a novel clue for studying determinants of microbial activities in other ecosystems.

Endogenous small intestinal microbiome determinants of transient colonisation efficiency by bacteria from fermented dairy products: a randomised controlled trial

BackgroundThe effects of fermented food consumption on the small intestine microbiome and its role on host homeostasis are largely uncharacterised as our knowledge on intestinal microbiota relies mainly on faecal samples analysis. We investigated changes in small intestinal microbial composition and functionality, short chain fatty acid (SCFA) profiles, and on gastro-intestinal (GI) permeability in ileostomy subjects upon the consumption of fermented milk products.ResultsWe report the results from a randomised, cross-over, explorative study where 16 ileostomy subjects underwent 3, 2-week intervention periods. In each period, they consumed either milk fermented by Lacticaseibacillus rhamnosus CNCM I-3690, or milk fermented by Streptococcus thermophilus CNCM I-1630 and Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519, or a chemically acidified milk (placebo) daily. We performed metataxonomic, metatranscriptomic analysis, and SCFA profiling of ileostomy effluents as well as a sugar permeability test to investigate the microbiome impact of these interventions and their potential effect on mucosal barrier function. Consumption of the intervention products impacted the overall small intestinal microbiome composition and functionality, mainly due to the introduction of the product-derived bacteria that reach in several samples 50% of the total microbial community. The interventions did not affect the SCFA levels in ileostoma effluent, or gastro-intestinal permeability and the effects on the endogenous microbial community were negligible. The impact on microbiome composition was highly personalised, and we identified the poorly characterised bacterial family, Peptostreptococcaceae, to be positively associated with a low abundance of the ingested bacteria. Activity profiling of the microbiota revealed that carbon- versus amino acid-derived energy metabolism of the endogenous microbiome could be responsible for the individual-specific intervention effects on the small intestine microbiome composition and function, reflected also on urine microbial metabolites generated through proteolytic fermentation.ConclusionsThe ingested bacteria are the main drivers of the intervention effect on the small intestinal microbiota composition. Their transient abundance level is highly personalised and influenced by the energy metabolism of the ecosystem that is reflected by its microbial composition (http://www.clinicaltrials.gov, ID NCT NCT02920294).3z8GaJs8-4AmNdyX8busiEVideo

Fine-scale evaluation of two standard 16S rRNA gene amplicon primer pairs for analysis of total prokaryotes and archaeal nitrifiers in differently managed soils.

The advance of high-throughput molecular biology tools allows in-depth profiling of microbial communities in soils, which possess a high diversity of prokaryotic microorganisms. Amplicon-based sequencing of 16S rRNA genes is the most common approach to studying the richness and composition of soil prokaryotes. To reliably detect different taxonomic lineages of microorganisms in a single soil sample, an adequate pipeline including DNA isolation, primer selection, PCR amplification, library preparation, DNA sequencing, and bioinformatic post-processing is required. Besides DNA sequencing quality and depth, the selection of PCR primers and PCR amplification reactions arguably have the largest influence on the results. This study tested the performance and potential bias of two primer pairs, i.e., 515F (Parada)-806R (Apprill) and 515F (Parada)-926R (Quince) in the standard pipelines of 16S rRNA gene Illumina amplicon sequencing protocol developed by the Earth Microbiome Project (EMP), against shotgun metagenome-based 16S rRNA gene reads. The evaluation was conducted using five differently managed soils. We observed a higher richness of soil total prokaryotes by using reverse primer 806R compared to 926R, contradicting to in silico evaluation results. Both primer pairs revealed various degrees of taxon-specific bias compared to metagenome-derived 16S rRNA gene reads. Nonetheless, we found consistent patterns of microbial community variation associated with different land uses, irrespective of primers used. Total microbial communities, as well as ammonia oxidizing archaea (AOA), the predominant ammonia oxidizers in these soils, shifted along with increased soil pH due to agricultural management. In the unmanaged low pH plot abundance of AOA was dominated by the acid-tolerant NS-Gamma clade, whereas limed agricultural plots were dominated by neutral-alkaliphilic NS-Delta/NS-Alpha clades. This study stresses how primer selection influences community composition and highlights the importance of primer selection for comparative and integrative studies, and that conclusions must be drawn with caution if data from different sequencing pipelines are to be compared.

Bacterial cell immobilized packed bed reactor for the elimination of dissolved organics from biologically treated post-tanning wastewater and its microbial community profile

In conventional, the biologically treated tannery wastewaters are rich in dissolved organics and the application of reverse osmosis (RO) to biologically treated tannery wastewater was challenged with fouling and failure of RO membrane due to existence of lingering dissolved organic compounds. In present investigation the bacterial cell immobilized packed bed reactor (CIPBR) was operated to remove the dissolved organic compounds in biologically treated post-tanning wastewater to avoid membrane fouling in RO. The efficient microbial syndicate to eliminate dissolved organics in post-tanning wastewater was isolated and immobilized on to the carbon silica matrix (CSM) in the range of 2.98 ± 0.2 × 107 cells gm−1 of CSM and the same was used as a carrier matrix in the packed bed reactor. The CIPBR established the CODtot, CODdis and BOD removal efficiency by 61 ± 4%, 57 ± 4% and 87 ± 3% respectively with CODtot, CODdis and BOD remained in the treated wastewater as 236 ± 21 mg/L, 228 ± 21 mg/L, and 12 ± 3 mg/L under continuous operation. The removal of dissolved organic compounds from the post-tanning wastewater was confirmed using UV–Visible and FT-IR spectroscopic studies. Among the total microbial community, the phylum Proteobacteria played most abundant role with 48.47% of relative abundance for the removal of dissolved organics in biologically treated post-tanning wastewater. The significance of the study is to replace the tertiary treatment unit operation in the conventional ETP/CETP to remove dissolved organics in wastewater.

한국 전통발효식품과 마이크로바이옴

Traditional food fermentation involves complex microbial community and their interactions. Despite the beneficial properties of these microbes, their complexity remains a challenge in predicting the key players involved in fermentation. Technological advancements in meta-omics approaches such as metataxonomics, metagenomics, and metatranscriptomics enable scientists to identify the total microbial community and their functions during different stages of fermentation. In the present study, we have discussed different Korean fermented foods and key microbes during fermentation, identified using next generation sequencing (NGS) techniques.

Evidence for Psammotermes allocerus termite nests as refugium for plant pathogenic microbes: a contribution to generation and maintenance of fairy circles in the Namib Desert

Fairy circles are circular, barren structures in dry grasslands and the mechanisms generating and maintaining them are currently under intense discussion. Here, we analysed bacterial and fungal communities in Namib Desert fairy circle soils, in the tapetum lining of termite nests, the gut of the prevailing sand termite Psammotermes allocerus, and also in the neighbouring grass plants. The total and active microbial communities were analysed through amplicon sequencing of both DNA and RNA extracts, respectively, species-specific PCRs, and through cultivation of bacteria and fungi from the various samples. In the sandy soils, the active bacterial communities were substantially different from the total communities, which suggested the fairy circle soils to be highly selective environments in comparison to other drylands or even temperate soils. This appears to be even more true for fungi as amplification of fungal genes from RNA extracts was not possible. However, we observed a large diversity among cultured fungal species in comparison to cultured bacterial species, specifically in tapetum samples. Our results support the hypothesis that Psammotermes allocerus acts as a vector for plant pathogenic fungi and that their nests below the bare patches of fairy circles provide a refugium for the fungal plant pathogens.

Rhodotorula glutinis как компонент биопленок навозных стоков

Analysis of manure biofilm effluents revealed an association of Clostridium ssp. (91.09 %), Escherichia coli (6.07), Bacteroides sp. (1.06), Sarcina ventriculi (0.91), Klebsiella sp. (0.14 %), and yeast Rhodotorula glutinis in the amount of 0.11 % of the total number of microorganisms. The pigmented yeast Rhodotorula glutinis has a low biochemical activity and is resistant to pH changes. In a natural environment (pH 7.0 ±0.3), the amount of Rhodotorula glutinis was 0.11% of the total number of micro- organisms (7*104±2.2 CFU/ml), but with a pH shift to 5.5±0.1 (acidification was carried out with 10 % sulfuric acid solution), the amount of yeast increased to 1.01 % (9*105±1.1 CFU/ml). Yeast of this species retains its viability when the temperature rises, so when heated to 70o C (in bioreactor plants when separating manure effluents), the amount of yeast was 0.06 % of the total microbial community (3*102±1.2 CFU/ml). The detection of yeast Rhodotorula glutinis in pig manure drains has not been described in the domestic and foreign literature before, their role requires further research.

Skin Barrier Function and the Microbiome.

Human skin is the largest organ and serves as the first line of defense against environmental factors. The human microbiota is defined as the total microbial community that coexists in the human body, while the microbiome refers to the collective genome of these microorganisms. Skin microbes do not simply reside on the skin but interact with the skin in a variety of ways, significantly affecting the skin barrier function. Here, we discuss recent insights into the symbiotic relationships between the microbiome and the skin barrier in physical, chemical, and innate/adaptive immunological ways. We discuss the gut-skin axis that affects skin barrier function. Finally, we examine the effects of microbiome dysbiosis on skin barrier function and the role of these effects in inflammatory skin diseases, such as acne, atopic dermatitis, and psoriasis. Microbiome cosmetics can help restore skin barrier function and improve these diseases.

Pattern changes of microbial communities in urban river affected by anthropogenic activities and their environmental driving mechanisms

The microbial community structure of sediments in the Bahe River Basin, China was studied using a high-throughput sequencing platform and PCR amplification to investigate the pattern changes in microbial communities in urban rivers affected by anthropogenic activities and their environmental driving mechanisms. The results demonstrated that the average total nitrogen and total phosphorus in the sediments were 524 and 734 mg/kg, respectively. The T, COD and {text{NH}}_{4}^{ + }-N of the water and the moisture content of the sediments has significantly impacted on the microbial community structure. Twenty microbial species with a relative abundance > 1% in the sediments of the river were observed, accounting for 95–99% of the total microbial community. The primary species were Proteobacteria (13.86–69.14%), Firmicutes (1.45–58.33%), Chloroflexi (3.68–26.18%), Actinobacteria (2.7–21.51%), Acidobacteria (0.73–16.36%), Bacteroides (1.53–14.11%), and Thermodesulfobacteria (0.1–8.9%), accounting for over 90% of the total microbial community. At the class level, the primary species were γ-proteobacteria, Alphaproteobacteria, Anaerolineae, Bacillus, Bacteroidota, Actinobacteriota, and Clostridia, accounting for over 70% of the total microbial community. Our results provide direct evidence for a link between microbial community structure and environment factors. This evidence demonstrates that sediment microorganisms can be applied to evaluate urban rivers pollution levels, which can provide a scientific basis for pollution control and management in the urban river affected by human activities.

Differential Timing for Glucose Assimilation in Prochlorococcus and Coexistent Microbial Populations in the North Pacific Subtropical Gyre.

ABSTRACTThe marine cyanobacterium Prochlorococcus can utilize glucose as a source of carbon. However, the relative importance of inorganic and organic carbon assimilation and the timing of glucose assimilation are still poorly understood in these numerically dominant cyanobacteria. Here, we investigated whole microbial community and group-specific primary production and glucose assimilation using incubations with radioisotopes combined with flow cytometry cell sorting. We also studied changes in the microbial community structure in response to glucose enrichments and analyzed the transcription of Prochlorocccus genes involved in carbon metabolism and photosynthesis. Our results showed a diel variation for glucose assimilation in Prochlorococcus, with maximum assimilation at midday and minimum at midnight (~2-fold change), which was different from that of the total microbial community. This suggests that the timing in glucose assimilation in Prochlorococcus is coupled to photosynthetic light reactions producing energy, it being more convenient for Prochlorococcus to show maximum glucose uptake precisely when the rest of microbial populations have their minimum glucose uptake. Many transcriptional responses to glucose enrichment occurred after 12- and 24-h periods, but community composition did not change. High-light Prochlorococcus strains were the most impacted by glucose addition, with transcript-level increases observed for genes in pathways for glucose metabolism, such as the pentose phosphate pathway, the Entner-Doudoroff pathway, glycolysis, respiration, and glucose transport. While Prochlorococcus C assimilation from glucose represented less than 0.1% of the bacterium’s photosynthetic C fixation, increased assimilation during the day and glcH gene upregulation upon glucose enrichment indicate an important role of mixotrophic C assimilation by natural populations of Prochlorococcus.IMPORTANCE Several studies have demonstrated that Prochlorococcus, the most abundant photosynthetic organism on Earth, can assimilate organic molecules, such as amino acids, amino sugars, ATP, phosphonates, and dimethylsulfoniopropionate. This autotroph can also assimilate small amounts of glucose, supporting the hypothesis that Prochlorococcus is mixotrophic. Our results show, for the first time, a diel variability in glucose assimilation by natural populations of Prochlorococcus with maximum assimilation during midday. Based on our previous results, this indicates that Prochlorococcus could maximize glucose uptake by using ATP made during the light reactions of photosynthesis. Furthermore, Prochlorococcus showed a different timing of glucose assimilation from the total population, which may offer considerable fitness advantages over competitors “temporal niches.” Finally, we observed transcriptional changes in some of the genes involved in carbon metabolism, suggesting that Prochlorococcus can use both pathways previously proposed in cyanobacteria to metabolize glucose.