Bacterial OTUs Research Articles

The Core of Gut Life: Firmicutes Profile in Patients with Relapsing-Remitting Multiple Sclerosis.

The multiple sclerosis (MS) incidence rate has been increasing in Russia, but the information about the gut bacteriobiome in the MS-afflicted patients is scarce. Using the Illumina MiSeq sequencing of 16S rRNA gene amplicons, we aimed to analyze the Firmicutes phylum and its taxa in a cohort of Moscow patients with relapsing-remitting MS, assessing the effects of age, BMI, disease modifying therapy (DMT), disability (EDSS), and gender. Among 1252 identified bacterial OTUs, 857 represented Firmicutes. The phylum was the most abundant also in sequence reads, overall averaging 74 ± 13%. The general linear model (GLM) analysis implicated Firmicutes/Clostridia/Clostridiales/Lachospiraceae/Blautia/Blautia wexlerae as increasing with BMI, and only Lachospiraceae/Blautia/Blautia wexlerae as increasing with age. A marked DMT-related decrease in Firmicutes was observed in females at the phylum, class (Clostridia), and order (Clostridiales) levels. The results of our study implicate DMT and gender as factors shaping the fecal Firmicutes assemblages. Together with the gender-dependent differential MS incidence growth rate in the country, the results suggest the likely involvement of gender-specific pathoecological mechanisms underlying the occurrence of the disease, switching between its phenotypes and response to disease-modifying therapies. Overall, the presented profile of Firmicutes can be used as a reference for more detailed research aimed at elucidating the contribution of this core phylum and its lower taxa into the etiology and progression of relapsing-remitting multiple sclerosis.

Revealing interactions between root phenolic metabolomes and rhizosphere bacterial communities in Populus euphratica plantations

How the root metabolic profiles and rhizosphere bacterial communities of dioecious plants respond to soil properties and sex identity is largely unknown. In this study, we analyzed root phenolic metabolomes and rhizosphere bacterial microbiomes of Populus euphratica females and males in two P. euphratica plantations with different soil properties to reveal the relative importance of soil and sex effects, and to decipher associations of certain phenolic compounds with specific bacterial taxa. We found that the relative abundances of bacterial OTUs and phenolic metabolites were closely linked to soil properties and sex identity. Soil is the main filter influencing the root phenolic metabolic profiles and rhizosphere bacterial communities of P. euphratica, while sexes and their interactions with soil properties are secondary factors. Differences in the diversity and evenness of phenolic metabolites were affected by plant sex, but not by soil properties. Conversely, the diversity and evenness of bacterial communities were affected by soil properties independent of plant sex. A multiple regression model indicated the presence of associations between root phenolic metabolites and specific soil bacteria taxa. Furthermore, all bacterial phyla and families correlated with at least one phenolic metabolite. Especially, both Nitrosomonadaceae and Cytophagaceae positively correlated with salicylic acid. Thus, our study provides new insights into the ecological mechanism that maintains rhizosphere bacterial communities in P. euphratica plantations in the desert area.

Running after ghosts: are dead bacteria the dark matter of the human gut microbiota?

ABSTRACT The human gut microbiota has been explored by a wide range of culture-dependent and culture-independent methods, revealing that many microbes remain uncharacterized and uncultured. In this work, we aimed to confirm the hypothesis that some of the species present in the human gut microbiota remain uncultured not because of culture limitations, but because all members of such species are dead before reaching the end of the gastro-intestinal tract. We evaluate this phenomenon by studying the microbial viability and culturability of the human gut microbiota from the fresh fecal materials of eight healthy adults. For the first time, we applied fluorescence-activated cell sorting (FACS) combined with 16S metagenomics analysis and microbial culturomics. We identified a total of 1,020 bacterial OTUs and 495 bacterial isolates through metagenomics and culturomics, respectively. Among the FACS metagenomics results, only 735 bacterial OTUs were alive, comprising on average 42% of known species and 87% of relative abundance per individual. The remaining uncultured bacteria were rare, dead, or injured. Our strategy allowed us to shed light on the dark matter of the human gut microbiota and revealed that both metagenomics and culturomics approaches are needed for greater insight into the diversity and richness of bacteria in the human gut microbiota. Further work on culture is needed to enhance the repertoire of cultured gut bacteria by targeting low abundance bacteria and optimizing anaerobic sample conditioning and processing to preserve the viability of bacteria.

Autotoxic effects of applied vanillic acid on Dynamic succession of soil microbial community

We studied the degradation of vanillic acid in soil was studied by high performance liquid chromatography and gas chromatography. Illumina MISEQ high-throughput sequencing was used to identify the abundance of bacteria and fungi in soil. The results showed that when the concentration of vanillic acid decreased to a certain level in the soil, its degradation rate became slow. The application of vanillic acid gradually decreased the total number of bacterial OTUs in soil, while the total number of fungal OTUs increased. At the same time, the richness and diversity of bacteria were always higher than fungi. Key microbial taxa at different degradation stages of vanillic acid were identified at the phylum and genus level, including bacteria (<i>Proteobacteria, Firmicutes, Actinobacteria, Chloroflexi, Methylibium, Methylobacillus, Aeromicrobium, Pseudonocardia</i>) and Fungi (<i>Ascomycota, Zygomycota, Basidiomycota, Rhodotorula, Mortierella

Diversity of the Bacterial Community of Three Soils Revealed by Illumina-Miseq Sequencing of 16S rRNA Gene in the South of Brazzaville, Congo

The study was conducted on three soils (MFILOU, SNR and ORSTOM) at the south of Brazzaville in Congo. The aim of the work was to study the composition and diversity of the soil microbial community. Microbial diversity was assessed using the Miseq-Sequencing. The results showed that microbial diversity was represented by 1289 OTUs assigned to the Bacteria (1282 OTUs), Fungi (2 OTUs), Viridiplantae (3 OTUs) and metazoa (2OTUs) domain with 97% of similarity. The 1282 bacterial OTUs were affiliated with 12 phyla, 31 classes, 59 orders, 122 families, 288 genera et 521 species for all sites. The Proteobacteria (45.59%-29.92%), Firmicutes (27.27%-7.35%), Acidobacteria (16.74%-10.15%), Actinobacteria (12.35%-5.07%) and Nitrospirae are the most abundant common phyla for the three sites. The most dominant common classes were Alphaproteobacteria (38.87%-24.77%), Bacilli (27.20%-6.95%), Acidobacteria (16.47%-7.59%), Actinobacteria (12.35%-5.07%) and Nitrospira (9.81%-1.78%). The most abundant common orders for the 3 sites are represented by Rhizobiales (33.96%-20.38%), Bacillales (27.20%-6.95%), Acidobacteriales (16.49%-7.61%), Actinomycetales (10.20%-3.6%) and Nitrospirales (9.81%-1.78%). Bacillaceae (25.37%-5.60%), Acidobacteriaceae (16.49%-7.61%), Bradyrhizobiaceae (10.81%-4.61%), Nitrospiraceae (9.81%-1.78%) and Chitinophagaceae (4.24%-1.59%) were the best distributed common families in the microbial community of the three sites. Bacillus (25.27%-5.56%), yhe most abundant and common genera were Rhodoplanes (15.48%-5.30%), Bradyrhizobium (10.74%-4.39%), Nitrospira (9.81%-1.78%) and Acidobacterium (8.49%-6.51%). At species level, Rhodoplanes spp. (15.26%-5.10%), Bradyrhizobium spp. (10.59%-4.35%) and Acidobacterium spp. (8.49%-6.51%) were the most common and abundant in the three soils.

Comparative Microbiome and Metabolome Analyses of the Marine Tunicate Ciona intestinalis from Native and Invaded Habitats.

Massive fouling by the invasive ascidian Ciona intestinalis in Prince Edward Island (PEI, Canada) has been causing devastating losses to the local blue mussel farms. In order to gain first insights into so far unexplored factors that may contribute to the invasiveness of C. intestinalis in PEI, we undertook comparative microbiome and metabolome studies on specific tissues from C. intestinalis populations collected in invaded (PEI) and native regions (Helgoland and Kiel, Germany). Microbial community analyses and untargeted metabolomics revealed clear location- and tissue-specific patterns showing that biogeography and the sampled tissue shape the microbiome and metabolome of C. intestinalis. Moreover, we observed higher microbial and chemical diversity in C. intestinalis from PEI than in the native populations. Bacterial OTUs specific to C. intestinalis from PEI included Cyanobacteria (e.g., Leptolyngbya sp.) and Rhodobacteraceae (e.g., Roseobacter sp.), while populations from native sampling sites showed higher abundances of e.g., Firmicutes (Helgoland) and Epsilonproteobacteria (Kiel). Altogether 121 abundant metabolites were putatively annotated in the global ascidian metabolome, of which 18 were only detected in the invasive PEI population (e.g., polyketides and terpenoids), while six (e.g., sphingolipids) or none were exclusive to the native specimens from Helgoland and Kiel, respectively. Some identified bacteria and metabolites reportedly possess bioactive properties (e.g., antifouling and antibiotic) that may contribute to the overall fitness of C. intestinalis. Hence, this first study provides a basis for future studies on factors underlying the global invasiveness of Ciona species.

The microbial community structure of the Dupnisa cave in Kırklareli, Turkey

Cave ecosystems count to be extreme environments due to their stable temperature, darkness, high humidity rates, and limited organic materials. In this context, these ecosystems represent invaluable laboratories for microbiological studies. Although there are common features between the microorganism groups obtained from the culture-based microbiological studies conducted in the caves and the groups highlighted through molecular methods, the microorganism groups determined through this last method are richer. The detected microorganisms are variable depending on the characteristics of each cave. The aim of this study is to determine the microbial diversity in samples taken from 5 different regions (including regions visited by tourists) of Dupnisa Cave and to reveal the differences between these regions. This is the first microbiological study running in cave sediments of Dupnisa Cave System situated in the north-western of Turkey. In this study, using the Illumina MiSeq next-generation sequencing approach for analyses of Dupnisa Cave samples, 14 phyla and 298 genera as well as 2 phyla and 20 genera can be attributed to bacterial and archaea OTUs, respectively. Moreover, the bacterial community is dominated by the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Gemmatimonadetes, Firmicutes, Nitrospirae, Chloroflexi and Acidobacteria distributed with 1 % and above. Archaeal community is represented by Thaumarchaeota and Euryarchaeota phyla. Proteobacteria is the most dominant bacterial phylum and Thaumarchaeota dominates the archaeal phyla. The highest number of types of bacteria according to Chao 1 richness estimation index were found at point AF (cave entrance / sediment), and that of types of archaea were found at point F2 (touristic area 2 / cave sediment). F2 was determined as the sampling point with the highest diversity of archaeal and bacterial genera according to Shannon-Wiener diversity index.

Active phoD-harboring bacteria are enriched by long-term organic fertilization

PhoD-harboring microorganisms are crucial for the regulation of soil phosphorus (P) cycling through the secretion of alkaline phosphomonoesterases and are also known to be sensitive to fertilizer inputs. However, the impacts of long-term mineral and organic fertilizer inputs on active phoD-harboring functional communities in soils remain largely unknown. In the present study, 18O-DNA-stable isotope probing coupled with high-throughput sequencing was utilized in order to characterize active phoD-harboring functional bacterial communities in soils subjected to long-term no-fertilizer (Control), mineral-only fertilizer (NPK), organic-only fertilizer (M), and the combination of mineral and organic fertilizer (NPKM) amendments. Total and active phoD gene abundance decreased in soils amended with long-term mineral fertilizer, but increased in soils under organic fertilizer amendment, compared with the non-fertilized soils. A total of 51 active phoD-harboring bacterial OTUs, mainly belonging to Actinobacteria, were identified in this study. Organically amended soils harbored a higher diversity of active bacterial community. In the active phoD-harboring functional community, Rhodococcus comprised approximately 99% of the total relative abundance in the unfertilized soil, whereas Nocardiopsis and Bacillus accounted for approximately 62% and 24%, respectively, in mineral-only fertilized soils. Active phoD-harboring communities were dominated by members of the genera Streptomyces (26–60%), Nocardia (5–9%) and Gordonia (23–41%) in all organically fertilized soils, including M and NPKM. Overall, these long-term fertilization regimes altered the abundance, richness and composition of the active phoD-harboring functional microbial community. This study provides novel insights into the responses of the active functional bacterial community that is responsible for soil P mineralization to differing long-term fertilization regimes.

Disentangling the role of salinity-sodicity in shaping soil microbiome along a natural saline-sodic gradient

Increasing salinity and sodicity have been recognized as threats to soil fertility and crop yield worldwide. In recent years, salt-affected soils have received great attentions due to the shortage of arable land. This study therefore aims to characterize soil bacterial community, assembly process and co-occurrence network along natural saline-sodic gradients across Songnen Plain, Northeast China. As revealed by Miseq sequencing, 8482 bacterial OTUs were annotated at 97% identity across 120 soil samples. Our results indicated that soil salinity-sodicity not only significantly decreased bacterial richness and but also impacted bacterial community composition. The dominant bacterial phyla included Proteobacteria (28.89%), Actinobacteria (19.96%) and Gemmatimonadetes (16.71%). By applying threshold indicator species analysis (TITAN), OTUs from Gemmatimonadetes were found to be the taxa with the most prevalent and strongest preference for high salinity-sodicity. Null model analysis revealed that the majority (76.4%) of βNTI values were below −2 or above 2, indicating deterministic process was dominant across all samples. Notably, deterministic process contributed to a greater extent in higher saline-sodic soils. The bacterial co-occurrence network was more complex in slightly saline-sodic soils than in moderately and extremely saline-sodic soils, reflected by more nodes, more hubs and stronger connections, which was mainly driven by soil pH. These results provide strong evidence that salinity-sodicity was a key determinant in shaping soil bacterial community, assembly process and co-occurrence network pattern.

Metabarkodlama yaklaşımıyla Tuz Gölü, Türkiye mikroorganizmalarının belirlenmesi için bir pilot çalışma

Mikroskopi ve kültür tekniklerine dayanan geleneksel mikrobiyal yöntemler oldukça etkili olmalarına rağmen, çevresel örneklerde bulunan mikrobiyal türlerin yüksek çeşitliliğini tanımlamakta zaman zaman yetersiz kalmaktadır. Geçtiğimiz son yirmi yılda, moleküler teknikler önemli düzeyde gelişmiştir ve genomik yaklaşımlar mikroorganizmaların dağılımını daha kapsamlı ve nicel olarak tanımlamak için kullanılmaktadır. Bu pilot çalışmada, Tuz Gölü'nde bulunan prokaryotik ve ökaryotik mikroorganizmaların çeşitliliği metabarkodlama yaklaşımıyla araştırılmıştır. 16S / 18S rDNA dizilemesi sonuçlarına göre, örneklerde ortalama 29 arkeal, 23 bakteriyel ve 61 ökaryotik OTU belirlenmiştir ve prokaryotik OTU`ların oranı %65,3'tür. Tüm örneklerde, en çok belirlenen arkeal OTU Euryarchaeota şubesinden Haloquadratum walsbyi`e aittir ve en yaygın bakteriyel OTU`lar ise Salinibacter cinsinin üyelerine aittir. 18S rDNA sekanslama sonuçlarına göre, en çok gözlenen ökaryotik OTU, Dunaliella salina`dır. Bu çalışmada, in vitro kültürü yapılamayan birçok prokaryotik ve ökaryotik OTU tespit edilmiş ve veritabanlarındaki 16S rDNA sekanslarına % 97'den az benzerliği (% 92) olan bir OTU belirlenmiştir. Elde edilen sonuçlar, Tuz Gölü'ndeki mikrobiyal toplulukların yapısının ve bileşiminin aydınlatılmasına katkıda bulunma potansiyeline sahiptir.

Both artificial root exudates and natural Koelreuteria paniculata exudates modify bacterial community structure and enhance phenanthrene biodegradation in contaminated soils

Polycyclic aromatic hydrocarbons (PAHs) are environmental pollutants that represent a serious threat to the health of humans and ecosystems. The effects of plant root and artificial root exudates (ARE) on the biodegradation of phenanthrene (PHE) and their impact on soil bacterial community structure was the focus of this work using four treatments for 180 days. Treatments included; control treatment (CK), low concentration of ARE (AREL), high concentration of ARE (AREH), and planting Koelreuteria paniculata saplings (KOE). The diversity and composition of soil bacterial community were analyzed using high-throughput sequencing. The results showed that KOE treatments had the most significant effect on the biodegradation of PHE compared to controls. ARE treatments had the similar effects on the biodegradation of PHE in soil with high efficiency in AREH than AREL. Both KOE and ARE treatments reduced diversity of bacterial community but increased the abundance of PAHs degrading bacterial populations within representative phyla, including Proteobacteria and Firmicutes. During the study, the total bacterial OTUs showed the number of unique genus types initially increased, then lowered in the later stages of the incubation process. Specific bacterial populations enriched by the treatments and supported by the exudates seemed to determine the biodegradation of PHE and not the overall bacterial diversity.

The sputum microbiome associated with different sub-types of AECOPD in a Chinese cohort

BackgroundChronic obstructive pulmonary disease (COPD) is one of the most prevalent diseases worldwide. Episodes of acute exacerbations of COPD (AECOPD) are associated with disease severity and progression. Although substantial progress has been made in understanding the dynamics of AECOPD, little is known about the sputum microbiome of AECOPD in the Chinese population.MethodsIn this study, we characterized the sputum microbiomes from sputum specimens collected from healthy controls (n = 10), stable (n = 4), AECOPD (n = 36), and recovery (n = 18) stages by sequencing the V3-V4 region of the 16S rRNA gene with a HiSeq sequencer.ResultsStreptococcus was the most dominant genus among all the different types of sputum. A random forest model was developed to identify bacterial taxa that differentiate AECOPD samples from others. Most of the top predictors, except Pseudomonas, were less abundant in AECOPD samples. We also developed random forest models to differentiate subtypes of AECOPD based on blood eosinophil counts, the frequency of AECOPD, and sputum eosinophils. Bacterial taxa associated with Pasteurellaceae, Fusobacterium, Solobacterium, Haemophilus, Atopobium, Corynebacterium and Streptococcus, were enriched in the sputum microbiomes of eosinophilic AECOPD. Random forest models also demonstrate that a total of 2 bacterial OTUs were needed to differentiate frequent from non-frequent AECOPDs, and 23 OTUs were enough to accurately predict sputum-eosinophilic (sputum eosinophilic concentration ≥ 3%) AECOPD.ConclusionThis study expanded our understanding of the sputum microbiome associated with different subtypes and clinical status of patients with AECOPD in a Chinese cohort, which provides insights into novel and more targeted management of the different subtypes of AECOPD.

Predicting disease occurrence with high accuracy based on soil macroecological patterns of Fusarium wilt.

Soil-borne plant diseases are increasingly causing devastating losses in agricultural production. The development of a more refined model for disease prediction can aid in reducing crop losses through the use of preventative control measures or soil fallowing for a planting season. The emergence of high-throughput DNA sequencing technology has provided unprecedented insight into the microbial composition of diseased versus healthy soils. However, a single independent case study rarely yields a general conclusion predictive of the disease in a particular soil. Here, we attempt to account for the differences among various studies and plant varieties using a machine-learning approach based on 24 independent bacterial data sets comprising 758 samples and 22 independent fungal data sets comprising 279 samples of healthy or Fusarium wilt-diseased soils from eight different countries. We found that soil bacterial and fungal communities were both clearly separated between diseased and healthy soil samples that originated from six crops across nine countries or regions. Alpha diversity was consistently greater in the fungal community of healthy soils. While diseased soil microbiomes harbored higher abundances of Xanthomonadaceae, Bacillaceae, Gibberella, and Fusarium oxysporum, the healthy soil microbiome contained more Streptomyces Mirabilis, Bradyrhizobiaceae, Comamonadaceae, Mortierella, and nonpathogenic fungi of Fusarium. Furthermore, a random forest method identified 45 bacterial OTUs and 40 fungal OTUs that categorized the health status of the soil with an accuracy >80%. We conclude that these models can be applied to predict the potential for occurrence of F. oxysporum wilt by revealing key biological indicators and features common to the wilt-diseased soil microbiome.

Convergence, divergence or chaos? Consequences of tree trunk decay for pedogenesis and the soil microbiome in a temperate natural forest

The biochemical effects of trees may significantly influence local pedogenesis as well as pedocomplexity, biodiversity and forest dynamics on both stand and landscape scales. One such effect is the decay of tree trunks, which is driven by organisms, and especially by the microbiome. Decomposition modifies soil formation, which due to the existence of many feedbacks affects the composition of the decomposer community. We aimed to uncover general trends in the evolution of Entic Podzols as well as individual trajectories of soil properties below decaying beech trunks in an old-growth mountain forest. In particular, we used mathematical models to distinguish soil convergence, divergence and chaotic behaviour to enhance a general theory of pedogenesis. We further aimed to calculate the depth and time of convergence if this scenario is prevailing in the study plot. Pedogenetic pathways were assessed regarding the changing composition of fungal and bacterial communities in soils to obtain a complex picture of the decaying trunk-soil microbiome system.We sampled the decaying wood layer under 24 lying beech trunks and corresponding organic horizons on adjacent control microsites occupied by decaying beech leaves. At the same time we sampled underlying mineral soil horizons at both microsites (wood vs. leaves), all on Entic Podzols and granite (in total 192 soil samples). Individual trunk fall events were dated using precise dendrochronology, with the resulting chronosequence covering trunks lying for 8–52 years. We analysed decomposition processes (with a wide spectra of organic acids and ions analysed), soil chemistry (28 additional soil properties assessed), and the microbiome composition in both decaying organic matter and soils (relative abundances of the 200 most common bacterial and fungal OTUs analysed).During the first stage of trunk decay, underlying Entic Podzols responded with a significant increase of nutrients, pH, and CEC, and the maximal divergence compared to control sites was reached between 12 and 60 years after the trunk fall. Subsequently, a majority of soil properties slowly converged over a few decades to match the soil properties of control sites. The modelled convergence point occurred at ages between 39 (SO42−) and 229 (Alw) years, with a median convergence time of 53 years. The majority of soil properties converged within 20 cm below the trunk, but mathematical models predicted footprints of some soil properties down to depths of ca 60 cm. In addition, 11 soil properties did not converge at any depth, and for some properties the models even diverged. Differences in bacterial and fungal communities between below-trunk and control positions were relatively minor. Pedochemical drivers of fungal and bacterial communities (nutrients content, Ntot, Cox, Al, Fe, Mn forms) changed significantly in the mineral soil below trunks, and the microbiome partly reflected these depth-related changes. However, we propose that there is a threshold between organic and mineral soil horizons limiting the impacts of trunk decay and pedogenesis in changes to the microbiome.

Frog Skin Microbiota Vary With Host Species and Environment but Not Chytrid Infection.

Describing the structure and function of the amphibian cutaneous microbiome has gained importance with the spread of Batrachochytrium dendrobatidis (Bd), the fungal pathogen that can cause the skin disease chytridiomycosis. Sampling amphibian skin microbiota is needed to characterize current infection status and to help predict future susceptibility to Bd based on microbial composition since some skin microbes have antifungal capabilities that may confer disease resistance. Here, I use 16S rRNA sequencing to describe the composition and structure of the cutaneous microbiota of six species of amphibians. Frog skin samples were also tested for Bd, and I found 11.8% Bd prevalence among all individuals sampled (n = 76). Frog skin microbiota varied by host species and sampling site, but did not differ among Bd-positive and Bd-negative individuals. These results suggest that bacterial composition reflects host species and the environment, but does not reflect Bd infection among the species sampled here. Of the bacterial OTUs identified using an indicator species analysis as strongly associated with amphibians, significantly more indicator OTUs were putative anti-Bd taxa than would be expected based on the proportion of anti-Bd OTUs among all frog OTUs, suggesting strong associations between host species and anti-Bd OTUs. This relationship may partially explain why some of these frogs are asymptomatic carriers of Bd, but more work is needed to determine the other factors that contribute to interspecific variation in Bd susceptibility. This work provides important insights on inter- and intra-specific variation in microbial community composition, putative function, and disease dynamics in populations of amphibians that appear to be coexisting with Bd.

On distinguishing the natural and human-induced sources of airborne pathogenic viable bioaerosols: characteristic assessment using advanced molecular analysis

Ambient air consists of bioaerosols that constitute many microbes from biosphere due to natural and anthropogenic activities. Size-dependent ambient measurements of bioaerosols at two seminatural and three anthropogenic coastal sites in southern tropical India were taken during the summer 2017. All the five sites considered in this study considerably contributed to the bioaerosol burden with larger contribution from the dumping yard site followed by the marshland site, wastewater treatment plant, composting site, and Indian Institute of Technology Madras. The colony-forming units concentration for all the sites ranged from 17 to 2750 m−3 for bacteria and 42–2673 m−3 for fungi. Firmicutes and Actinomycetes were the dominant phyla observed in 698 bacterial OTUs obtained, and Ascomycota and Zygomycota were the dominant phyla observed in 159 fungal OTUs obtained in the study. Further, the study revealed the presence of pathogenic and ice-nucleating bacteria and fungi in the bioaerosols that can largely affect the well-being of the human population and vegetation in this region. Moreover, the statistical analysis revealed high bacterial abundance and diversity at the grit chamber of wastewater treatment plant and high fungal abundance and diversity at the dumping yard. Further, principal coordinate analysis of the sites studied inferred that the marshland, wastewater treatment plant, and the dumping yard sites shared similar microbial community composition indicating the existence of similar source materials and activities at the sites. Further, this study evidently brings out the fact that urban locations may play an important role in anthropogenic contribution of both pathogenic and ice-nucleating microorganisms.

High-Throughput Sequencing Reveals the Diversity and Community Structure in Rhizosphere Soils of Three Endangered Plants in Western Ordos, China.

China's western Ordos is a distribution area for the extremely precious remnants of ancient Asian environments, which in endangered plant species and complex ecosystems. Accordingly, in this study, we collect three endangered plants belonging to the Zygophyllaceae family, namely Tetraena mongolica, Sarcozygium xanthoxylon, and Nitraria tangutorum Bobr. High-throughput sequencing technology was applied to study microbial diversity in these plant rhizosphere soils. Analysis of species composition abundance, Alpha diversity, Beta diversity and microbial structure are analyzed. 2428 bacterial OTUs and 1256 fungal OTUs are obtained from the rhizosphere soils, and the bacterial and fungal sequencing coverage is above 99%. Bacilli are the most abundant (86.91%) in the bacterial community. The fungal community has significant differences in three plants. The abundances of the genus Dothideomycetes in the rhizosphere soils of Tetraenamongolica and Sarcozygium xanthoxylon plants are the highest, which are 44.57% and 37.69%, respectively. Thus, Dothideomycetes is the dominant bacteria in the community. The genus Sordariomycetes in the rhizosphere soil is the dominant fungi with a relative abundance of 41.04%. Redundancy analysis revealed that microbial communities were closely related to environmental factors. Overall, this study bring new insights into the relationship between rhizosphere soils microbial diversity and environment to improving the adaptability of theendangered plants in survival environment.

Potential utilization of terrestrially derived dissolved organic matter by aquatic microbial communities in saline lakes.

Lakes receive large amounts of terrestrially derived dissolved organic matter (tDOM). However, little is known about how aquatic microbial communities interact with tDOM in lakes. Here, by performing microcosm experiments we investigated how microbial community responded to tDOM influx in six Tibetan lakes of different salinities (ranging from 1 to 358 g/l). In response to tDOM addition, microbial biomass increased while dissolved organic carbon (DOC) decreased. The amount of DOC decrease did not show any significant correlation with salinity. However, salinity influenced tDOM transformation, i.e., microbial communities from higher salinity lakes exhibited a stronger ability to utilize tDOM of high carbon numbers than those from lower salinity. Abundant taxa and copiotrophs were actively involved in tDOM transformation, suggesting their vital roles in lacustrine carbon cycle. Network analysis indicated that 66 operational taxonomic units (OTUs, affiliated with Alphaproteobacteria, Actinobacteria, Bacteroidia, Bacilli, Gammaproteobacteria, Halobacteria, Planctomycetacia, Rhodothermia, and Verrucomicrobiae) were associated with degradation of CHO compounds, while four bacterial OTUs (affiliated with Actinobacteria, Alphaproteobacteria, Bacteroidia and Gammaproteobacteria) were highly associated with the degradation of CHOS compounds. Network analysis further revealed that tDOM transformation may be a synergestic process, involving cooperation among multiple species. In summary, our study provides new insights into a microbial role in transforming tDOM in saline lakes and has important implications for understanding the carbon cycle in aquatic environments.

Effects of Medicago sativa-Triticale wittmack intercropping system on rhizosphere soil nutrients and bacterial community in semi-arid region of NorthwestChina

Semi-arid region of Northwest China is characterized by barren soil, with high pH and high carbonate content. Saline-alkali land is easily formed in this area, which inhibits soil microbial activity and results in soil nutrient loss. To improve soil health in this area, effects of intercropping alfalfa and triticale on rhizosphere soil nutrients and bacterial community structure were examined though a three-consecutive-year experiment. The results showed that soil organic matter (SOM) content of alfalfa rhizosphere in intercropping was significantly higher than that in monoculture, while pH and available potassium (AK) content were lower than that in monoculture. The concentrations of SOM, available nitrogen (AN), available phosphate (AP) and AK of triticale rhizosphere in intercropping were significantly higher than those in monoculture. The bacterial sequences, OTUs, richness, and diversity of alfalfa and triticale in rhizosphere soil were all higher than those in monoculture. At phylum level, Proteobacteria and Bacteroidetes were dominant, accounting for 31.1%-33.4% and 22.4%-32.2% of the total OTUs, respectively. The relative abundance of Bacteroidete was higher in intercropping than in monoculture. Actinomycetes in the monoculture were significantly higher. Acidobacteria in the intercropping triticale was significantly higher than that in monoculture triticale. Verrucomicrobia in intercropping alfalfa was significantly more abundant than that in monoculture of alfalfa. At genus level, Algoriphagus, Flavobacterium, Gp6, and Chryseolinea in monoculture were greater than those in intercropping, and Cellvibrio showed an opposite trend. Results of correlation analysis showed that the abundance of Proteobacteria and Bacteroidetes were negatively correlated with soil pH, while that of Bacteroidetes were positively correlated with SOM, TN and AN. However, the abundance of Chloroflexi, Planctomycetes, Acidobacteria, Verrucomicrobia, and Gemmatimonadetes was negatively correlated with SOM and AN. Overall, alfalfa-triticale intercropping is an effective strategy to improve soil health in semi-arid region of Northwest China.

Bacterial and archaeal communities in deep sea waters near the Ninetyeast Ridge in Indian Ocean

Depth-dependent distribution patterns of bacterial and archaeal communities in deep sea water column around the Ninetyeast Ridge in the Indian Ocean were investigated using 16S rRNA gene profiling. Sampling was conducted at the northern Ninetyeast Ridge (1°59.89′N–9°59.70′S, 87°58.90′E–88°00.03′E) from September to November 2016 where samples were collected from the bathyal (1 000 m) to bathypelagic depths (>4 000 m) in four different stations. A total of 1 565 405 clean data falling into 6 712 bacterial OTUs and 1 452 727 clean data falling into 806 archaeal OTUs based on 97% similarity level were analyzed. Most of the bacterial 16S rRNA gene sequences were affiliated with Gammaproteobacteria, followed by Alphaproteobacteria and Bacteroidia. The archaeal 16S rRNA gene sequences mostly affiliated to Nitrososphaeria (Thaumarchaeota) dominated with relative abundances ranging from 52.68% to 97.2%, followed by Thermoplasmata (Euryarchaeota). Vertical partitioning of bacterial and archaeal communities among different water layers was observed. Canonical correspondence analysis (CCA) and Spearman’s correlations revealed that depth (P=0.003), dissolved oxygen (P=0.019), and nitrite (P=0.033) were the main environmental factors affecting bacterial community structure at genus level in the Ninetyeast Ridge. On the other hand, the first two CCA axes accounted for 74.4% of the explained total variance, it seems that the archaeal communities at genus level were heavily influenced by the environmental variables including depth, dissolved oxygen (DO), nitrite, salinity, phosphate, ammonia, nitrate, and silicate, but none of them exhibited any significant correlation on the structuring (P>0.1).