Diversity and distribution of the prokaryotic community in near-surface permafrost sediments in the Tianshan Mountains, China

The community structures and diversity of bacteria and archaea were investigated at 4 depths (1.5, 2.0, 2.5, and 3.0 m) in permafrost sediments in the Tianshan Mountains, using denaturing gradient gel electrophoresis of 16S rRNA gene amplified by polymerase chain reaction. Phylogenetic analysis of the dominant bands sequenced revealed the presence of rich diversity of bacteria, which could be related to the Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes, Bacteroidetes, Firmicutes, and Chloroflexi. The Proteobacteria, consisting of the alpha, beta, gamma and epsilon subdivisions, were clearly the dominant group at all depths studied. Archaeal diversity was relatively low and archaeal 16S rRNA gene sequences were grouped into 3 phylogenetic clusters within the 2 kingdoms Euryarchaeota and Crenarchaeota. Within the Euryarchaeota, methanogen-related group II was most abundant at shallow depth (1.5 m), whereas halobacterium-related group I dominated at greater depths. The low-temperature Crenarchaeota group was detected only at 2.5 and 3.0 m. Specific-depth distribution of methanogen-related Euryarchaeota group II and denitrifying bacteria of the genus Pseudomonas dominated at 1.5 m depth, accompanied by a distinct peak in the ratio of NH4-N to NO3/NO2-N, implying the potential capacity of these organisms in near-surface permafrost to release the greenhouse gases N2O and CH4.     

Exploring prokaryotic diversity in the genomic era

Our understanding of prokaryote biology from study of pure cultures and genome sequencing has been limited by a pronounced sampling bias towards four bacterial phyla - Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes - out of 35 bacterial and 18 archaeal phylum-level lineages. This bias is beginning to be rectified by the use of phylogenetically directed isolation strategies and by directly accessing microbial genomes from environmental samples.     

Monitoring bacterial communities in raw milk and cheese by culture-dependent and -independent 16S rRNA gene-based analyses

The diversity and dynamics of bacterial populations in Saint-Nectaire, a raw-milk, semihard cheese, were investigated using a dual culture-dependent and direct molecular approach combining single-strand conformation polymorphism (SSCP) fingerprinting and sequencing of 16S rRNA genes. The dominant clones, among 125 16S rRNA genes isolated from milk, belonged to members of the Firmicutes (58% of the total clones) affiliated mainly with the orders Clostridiales and the Lactobacillales, followed by the phyla Proteobacteria (21.6%), Actinobacteria (16.8%), and Bacteroidetes (4%). Sequencing the 16S rRNA genes of 126 milk isolates collected from four culture media revealed the presence of 36 different species showing a wider diversity in the Gammaproteobacteria phylum and Staphylococcus genus than that found among clones. In cheese, a total of 21 species were obtained from 170 isolates, with dominant species belonging to the Lactobacillales and subdominant species affiliated with the Actinobacteria, Bacteroidetes (Chryseobacterium sp.), or Gammaproteobacteria (Stenotrophomonas sp.). Fingerprinting DNA isolated from milk by SSCP analysis yielded complex patterns, whereas analyzing DNA isolated from cheese resulted in patterns composed of a single peak which corresponded to that of lactic acid bacteria. SSCP fingerprinting of mixtures of all colonies harvested from plate count agar supplemented with crystal violet and vancomycin showed good potential for monitoring the subdominant Proteobacteria and Bacteroidetes (Flavobacteria) organisms in milk and cheese. Likewise, analyzing culturable subcommunities from cheese-ripening bacterial medium permitted assessment of the diversity of halotolerant Actinobacteria and Staphylococcus organisms. Direct and culture-dependent approaches produced complementary information, thus generating a more accurate view of milk and cheese microbial ecology.     

Geographic distance and pH drive bacterial distribution in alkaline lake sediments across Tibetan Plateau

Continent-scale biogeography has been extensively studied in soils and marine systems, but little is known about biogeographical patterns in non-marine sediments. We used barcode pyrosequencing to quantify the effects of local geochemical properties and geographic distance for bacterial community structure and membership, using sediment samples from 15 lakes on the Tibetan Plateau (4-1670?km apart). Bacterial communities were surprisingly diverse, and distinct from soil communities. Four of 26 phyla detected were dominant: Proteobacteria, Bacteroidetes, Firmicutes and Actinobacteria, albeit 20.2% of sequences were unclassified at the phylum level. As previously observed in acidic soil, pH was the dominant factor influencing alkaline sediment community structure, phylotype richness and phylogenetic diversity. In contrast, archaeal communities were less affected by pH. More geographically distant sites had more dissimilar communities (r?=?0.443, P?=?0.030). Variance partitioning analysis showed that geographic distance (historical contingencies) contributed more to bacterial community variation (12.2%) than any other factor, although the environmental factors explained more variance when combined (28.9%). Together, our results show that pH is the best predictor of bacterial community structure in alkaline sediments, and confirm that both geographic distance and chemical factors govern bacterial biogeography in lake sediments.     

Diversity analyses of microbial communities in petroleum samples from Brazilian oil fields

Recent studies of oil fields have shown that the microbial diversity is represented by bacteria and archaea of wide distribution, and that many of these organisms have potential to metabolize organic and inorganic compounds. Biodegradation processes in oil industry are of great relevance, since it may be related with the loss of petroleum quality and can bring problems during production. The aim of this study was to compare the microbial communities present in biodegraded (GMR75) and non-biodegraded (PTS1) terrestrial oils from the Potiguar Basin (RN, Brazil) by using cultivation (microbial enrichments and isolation) and molecular approaches (16S rRNA gene libraries). The cultivated microorganisms recovered were affiliated with the phyla Actinobacteria, Firmicutes and Proteobacteria. Both bacterial 16S rRNA gene libraries revealed a great diversity, encompassing representatives from 8 different phyla (Actinobacteria, Bacteroidetes, Deferribacteres, Spirochaetes, Firmicutes, Proteobacteria, Thermotogae and Synergistetes) for the GMR75 sample, and from 5 different phyla (Actinobacteria, Chloroflexi, Firmicutes, Proteobacteria and Thermotoga) for the PTS1 sample. The archaeal 16S rRNA gene library was obtained only for GMR75 oil and all phylotypes were affiliated with the family Methanomicrobiaceae. Diversity results suggest that methanogenesis is the dominant terminal process for hydrocarbon degradation in GMR oil field, driven by anaerobic biodegradation.     

Characterization of the prokaryotic diversity in cold saline perennial springs of the Canadian high Arctic

The springs at Gypsum Hill and Colour Peak on Axel Heiberg Island in the Canadian Arctic originate from deep salt aquifers and are among the few known examples of cold springs in thick permafrost on Earth. The springs discharge cold anoxic brines (7.5 to 15.8% salts), with a mean oxidoreduction potential of -325 mV, and contain high concentrations of sulfate and sulfide. We surveyed the microbial diversity in the sediments of seven springs by denaturing gradient gel electrophoresis (DGGE) and analyzing clone libraries of 16S rRNA genes amplified with Bacteria and Archaea-specific primers. Dendrogram analysis of the DGGE banding patterns divided the springs into two clusters based on their geographic origin. Bacterial 16S rRNA clone sequences from the Gypsum Hill library (spring GH-4) were classified into seven phyla (Actinobacteria, Bacteroidetes, Firmicutes, Gemmatimonadetes, Proteobacteria, Spirochaetes, and Verrucomicrobia); Deltaproteobacteria and Gammaproteobacteria sequences represented half of the clone library. Sequences related to Proteobacteria (82%), Firmicutes (9%), and Bacteroidetes (6%) constituted 97% of the bacterial clone library from Colour Peak (spring CP-1). Most GH-4 archaeal clone sequences (79%) were related to the Crenarchaeota while half of the CP-1 sequences were related to orders Halobacteriales and Methanosarcinales of the Euryarchaeota. Sequences related to the sulfur-oxidizing bacterium Thiomicrospira psychrophila dominated both the GH-4 (19%) and CP-1 (45%) bacterial libraries, and 56 to 76% of the bacterial sequences were from potential sulfur-metabolizing bacteria. These results suggest that the utilization and cycling of sulfur compounds may play a major role in the energy production and maintenance of microbial communities in these unique, cold environments.     

A meta-analysis of the publicly available bacterial and archaeal sequence diversity in saline soils

An integrated view of bacterial and archaeal diversity in saline soil habitats is essential for understanding the biological and ecological processes and exploiting potential of microbial resources from such environments. This study examined the collective bacterial and archaeal diversity in saline soils using a meta-analysis approach. All available 16S rDNA sequences recovered from saline soils were retrieved from publicly available databases and subjected to phylogenetic and statistical analyses. A total of 9,043 bacterial and 1,039 archaeal sequences, each longer than 250 bp, were examined. The bacterial sequences were assigned into 5,784 operational taxonomic units (OTUs, based on ≥97 % sequence identity), representing 24 known bacterial phyla, with Proteobacteria (44.9 %), Actinobacteria (12.3 %), Firmicutes (10.4 %), Acidobacteria (9.0 %), Bacteroidetes (6.8 %), and Chloroflexi (5.9 %) being predominant. Lysobacter (12.8 %) was the dominant bacterial genus in saline soils, followed by Sphingomonas (4.5 %), Halomonas (2.5 %), and Gemmatimonas (2.5 %). Archaeal sequences were assigned to 602 OTUs, primarily from the phyla Euryarchaeota (88.7 %) and Crenarchaeota (11.3 %). Halorubrum and Thermofilum were the dominant archaeal genera in saline soils. Rarefaction analysis indicated that less than 25 % of bacterial diversity, and approximately 50 % of archaeal diversity, in saline soil habitats has been sampled. This analysis of the global bacterial and archaeal diversity in saline soil habitats can guide future studies to further examine the microbial diversity of saline soils.     

泥浸汁对太湖沉积物中的好氧可培养细菌多样性的影响

【目的】研究添加泥浸汁与否对太湖沉积物中可培养细菌的影响。【方法】采用R2A培养基和添加泥浸汁R2A培养基对沉积物中细菌进行分离培养,16S r RNA基因系统发育分析比较种群结构。【结果】培养基中添加泥浸汁,可使可培养细菌的种类数量增加到1.6倍。16S r RNA基因序列分析表明,培养的优势细菌类群存在明显差别。R2A培养基上生长的细菌主要为厚壁菌门(52%)、放线菌门(24%)、变形菌门(20%)和拟杆菌门(4%),其中大部分细菌与芽孢杆菌属、假单胞菌属、节杆菌属等关系密切;而添加泥浸汁的R2A培养基上生长的细菌则主要为变形菌门(40%)、放线菌门(35%)、厚壁菌门(22.5%)和拟杆菌门(2.5%),与鞘脂单胞菌属、芽孢杆菌属、副球菌属、节杆菌属等关系密切。【结论】添加泥浸汁原始营养因子可提高沉积物中可培养细菌的多样性,提高菌种可培养效率。     

大兴安岭典型永久冻土土壤细菌群落组成和多样性

【背景】土壤微生物是土壤生物中的重要成分,参与了土壤生态系统中关键的生物化学循环过程。但是关于寒温带多年冻土土壤微生物的研究还比较薄弱。【目的】探究大兴安岭多年冻土土壤中微生物的多样性和种群结构。【方法】利用MiSeq高通量测序技术对黑龙江大兴安岭地区呼中保护区落叶松冻土和樟子松林冻土土壤样品进行测序。【结果】在落叶松冻土和樟子松林冻土土壤中,相对丰度最高的优势菌群的组成基本一致,在门水平有疣微菌门(Verrucomicrobia)、变形菌门(Proteobacteria)、酸杆菌门(Acidobacteria)、浮霉菌门(Planctomycetes)、绿菌门(Chlorobi)、Parcubacteria、放线菌门(Actinobacteria)、拟杆菌门(Bacteroidetes)、厚壁菌门(Firmicutes)、芽单胞菌门(Gemmatimonadetes)10个细菌门类,其中,疣微菌门(Verrucomicrobia)在樟子松林土壤中的相对丰度较多,变形菌门(Proteobacteria)在落叶松林土壤中的相对丰度较多。通过α多样性分析可知,落叶松冻土土壤微生物的群落多样性高于樟子松林冻土,而且两者的细菌群落组成与结构差异性较大。【结论】为深入认识大兴安岭多年冻土区的土壤微生物群落结构组成以及影响因素提供数据支撑。     

Biofilm Bacterial Communities Inhabiting the Cave Walls of the Buda Thermal Karst System,Hungary

The diversity of biofilm bacterial communities associated with cave walls of the Buda Thermal Karst System (BTKS) located in Hungary was studied by scanning electron microscopy and molecular cloning based on 16S rRNA genes. Samples from two sites, the Molnár János cave (MJB) and the Rudas-Török spring cave (RTB), respectively, were analyzed and compared. The presence of iron precipitates was typical at both study sites, despite the fact that the cell morphological structure of the biofilms observed by SEM was characteristically different. Clones analyzed from BTKS were found to belong to 10 common phyla (Thermodesulfobacteria, Chloroflexi, Nitrospirae, Chlorobi, Proteobacteria, Firmicutes, Actinobacteria, Planctomycetes, Bacteroidetes, Verrucomicrobia) within the domain Bacteria. Moreover, sequences related to Aquificeae, Acidobacteria and Gemmatimonadetes were exclusive to MJB, while Cyanobacteria were found in RTB only. The phylogenetic distribution of the dominant bacterial clones was quite dissimilar between the two sites. In the biofilm from MJB clones affiliated with Firmicutes, whereas in the RTB clones related to Deltaproteobacteria were found in the highest number. In addition, substantially larger numbers of clone sequences related to thermophilic bacteria were recovered from MJB. On the basis of sequences of known microorganisms corresponding to our clone sequences, it is assumed that aerobic as well as anaerobic iron and sulfur transformation performed by different bacterial communities might be important biogenic processes in both caves.     

Spatial distribution of bacterial phylotypes in the gut of the termite Reticulitermes speratus and the bacterial community colonizing the gut epithelium

The bacterial community colonizing the gut wall of the termite Reticulitermes speratus was characterized without cultivation. Analysis of 16S rRNA genes after fractionation of the gut revealed that the bacterial composition on the gut wall was diverse and significantly different from that able to move unconfined in the gut fluid or physically associated with the gut protists. Actinobacteria, Firmicutes and Bacteroidetes were dominant on the gut wall, but Spirochaetes and the Termite group 1 phylum, abundant in the gut lumen, were relatively rare. A sequence-specific probe enabled the in situ detection of a rod-shaped Actinobacteria member, abundantly colonizing the gut paunch epithelium.     

中国南海沉积环境可培养细菌多样性研究

【目的】探索海洋沉积环境中可培养细菌的多样性。【方法】采用纯培养分离及16S rRNA基因序列鉴定的方法,对我国南海海域20个沉积物样品进行细菌多样性分析。【结果】共获得200株细菌,分属于47个属,99个种。经系统进化分析,可培养菌株主要分布于4个类群:厚壁菌门(Firmicutes)、变形菌门(Proteobacteria)、放线菌门(Actinobacteria)和拟杆菌门(Bacteroidetes),优势类群为Firmicutes,其中芽孢杆菌属(Bacillus)所占比例为55.6%;而Actinobacteria和Bacteroidetes两个类群获得菌株较少;在Firmicutes和Actinobacteria两个类群中发现8个潜在新种和3个潜在新属级类群。【结论】初步研究结果表明,南海海洋沉积环境可培养微生物资源丰富,新物种资源多样;其中,芽孢杆菌为海洋沉积环境中的优势类群,随着样品深度的增加,细菌多样性呈现递减的趋势,深度可能是影响细菌多样性的一个重要因素;其次,分离培养基和分离方法直接关系到样品中可培养微生物多样性的发现,有待深入研究。     

Differential abundance and core members of the bacterial community associated with wild male Zeugodacus cucurbitae fruit flies (Insecta: Tephritidae) from three geographical regions of Southeast Asia

Zeugodacus cucurbitae (Coquillet) is one of the most significant and widespread tephritid pest species of agricultural crops. This study reports the bacterial communities associated with Z. cucurbitae from three geographical regions in Southeast Asia (Thailand, Peninsular Malaysia, and Sarawak). The bacterial microbiota were investigated by targeted 16S rRNA gene (V3–V4 region) sequencing using the Illumina Mi-Seq platform. At 97% similarity and filtering at 0.001%, there were seven bacterial phyla and unassigned bacteria, comprising 11 classes, 23 orders, 39 families and 67 genera. The bacterial diversity and richness varied within and among the samples from the three geographical regions. Five phyla were detected for the Sarawak sample, and six each for the Thailand and Peninsular Malaysia samples. Four phyla—Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria—were represented in all the fruit fly specimens, forming the core members of the bacterial community. Proteobacteria was the predominant phylum, followed by Bacteroidetes, Firmicutes, and Actinobacteria. Fifty-three genera were represented in the Thailand sample, 56 in the Peninsular Malaysia sample, and 55 in the Sarawak sample. Forty-two genera were present in all the three geographical regions. The predominant core members were order Enterobacteriales (Proeteobacteria), and family Enterobacteriaceae (Enterobacteriales). Klebsiella (Enterobacteriaceae) was the predominant genus and K. oxytoca the predominant species with all specimens having?>?10% relative abundance. The results indicate the presence of a great diversity as well as core members of the bacterial community associated with different populations of Z. cucurbitae.

     

Bacterial diversity and community structure in polygonal tundra soils from Samoylov Island, Lena Delta, Siberia

During the Arctic summer, bacteria are active above the permafrost in an environment with sharp temperature and oxygen gradients. The present study addressed the diversity and abundance of bacteria in soil layers near the surface and above the permafrost of the rim and center of a low-centered polygon in the Lena Delta, Siberia. 16S rRNA gene clone libraries revealed the presence of all major soil bacterial groups and of the candidate divisions OD1, OP5, and OP11, and indicated a small-scale heterogeneity of these polygonal tundra soils. The diversity at the top of the elevated polygon rim was significantly different from that of the bottom and from both water-saturated sites of the polygon's center. The overall species-level diversity was very high (Shannon index of 5.3) but varied within the sites and decreased towards the permafrost table, coinciding with decreasing dissolved organic carbon (DOC) and phosphate concentrations. According to the number of operational taxonomical units (OTUs) and cells visualized by fluorescence in-situ hybridization, Bacteroidetes and Actinobacteria were the dominant members of the bacterial community in all sites. Bacteroidetes contributed almost 50% to all Bacteria cells while sequences affiliated with Bacteroidetes/Chlorobi represented on average 23% of all OTUs. Our results provide evidence of the extremely diverse bacterial communities present in permafrost soils and of the influence of nutrient concentrations, oxygen, and DOC on diversity.     

模拟氮沉降和降雨变化对贝加尔针茅草原土壤细菌群落结构的影响

研究氮沉降和降雨变化对土壤细菌群落结构的影响,对未来预测多个气候变化因子对草地生态系统影响的交互作用具有重要意义。以施氮和灌溉分别模拟氮沉降和降雨增加,采用高通量测序技术,研究8个氮添加水平(0、15、30、50、100、150、200、300kg N hm-2a-1)和2个水分添加水平(不灌溉、模拟夏季增雨100 mm灌溉)对土壤细菌群落结构的影响。结果表明,氮素和水分输入增加后,土壤细菌群落组成、丰度均显著变化(P0.05)。在群落中占主导的细菌门类有疣微菌门Verrucomicrobia(30.61%—48.51%)、变形菌门Proteobacteria(21.37%—29.97%)、酸杆菌门Acidobacteria(9.54%—20.67%)和拟杆菌门Bacteroidetes(4.96%—9.74%)。在常规降雨和水分添加两种条件下,随着氮添加水平的增加,占主导的细菌门类(相对丰度1%)表现出不同的变化趋势。疣微菌门相对丰度在常规降雨N100—N300条件下显著降低,但在氮素和水分同时添加条件下随氮添加水平升高而逐渐升高,在N200—N300时显著升高。变形菌门和拟杆菌门相对丰度在常规降雨高氮添加条件下呈升高趋势,但在水分添加时却无明显变化。酸杆菌门相对丰度在常规降雨高氮添加条件下升高,但在水分添加后呈明显下降趋势。放线菌门Actinobacteria相对丰度在常规降雨N100—N300条件下显著升高,但在水分添加后高氮添加时显著降低。厚壁菌门Firmicutes相对丰度在常规降雨条件下无显著变化,但在水分和高氮添加条件下降低。浮霉菌门Planctomycetes相对丰度在两种不同的水分添加条件下均呈先升高后降低的趋势。氮素和水分添加对土壤细菌群落结构的变化存在明显的互作效应(P0.0001)。在不同氮素和水分输入条件下共有19个土壤细菌门类相对丰度有显著差异。土壤细菌群落结构的变化主要来自于疣微菌门和酸杆菌门的相对丰度变化,两者可作为土壤细菌群落结构变化的指示种。综上,氮素和水分添加显著改变了土壤细菌群落结构,氮素和水分对土壤细菌不同门类相对丰度变化存在明显的互作效应。     

Response of Archaeal and Bacterial Soil Communities to Changes Associated with Outdoor Cattle Overwintering

Archaea and bacteria are important drivers for nutrient transformations in soils and catalyse the production and consumption of important greenhouse gases. In this study, we investigate changes in archaeal and bacterial communities of four Czech grassland soils affected by outdoor cattle husbandry. Two show short-term (3 years; STI) and long-term impact (17 years; LTI), one is regenerating from cattle impact (REG) and a control is unaffected by cattle (CON). Cattle manure (CMN), the source of allochthonous microbes, was collected from the same area. We used pyrosequencing of 16S rRNA genes to assess the composition of archaeal and bacterial communities in each soil type and CMN. Both short- and long- term cattle impact negatively altered archaeal and bacterial diversity, leading to increase of homogenization of microbial communities in overwintering soils over time. Moreover, strong shifts in the prokaryotic communities were observed in response to cattle overwintering, with the greatest impact on archaea. Oligotrophic and acidophilic microorganisms (e.g. Thaumarchaeota, Acidobacteria, and α-Proteobacteria) dominated in CON and expressed strong negative response to increased pH, total C and N. Whereas copiotrophic and alkalophilic microbes (e.g. methanogenic Euryarchaeota, Firmicutes, Chloroflexi, Actinobacteria, and Bacteroidetes) were common in LTI showing opposite trends. Crenarchaeota were also found in LTI, though their trophic interactions remain cryptic. Firmicutes, Bacteroidetes, Methanobacteriaceae, and Methanomicrobiaceae indicated the introduction and establishment of faecal microbes into the impacted soils, while Chloroflexi and Methanosarcinaceae suggested increased abundance of soil-borne microbes under altered environmental conditions. The observed changes in prokaryotic community composition may have driven corresponding changes in soil functioning.     

Bacterial and archaeal diversity in two hot spring microbial mats from the geothermal region of Tengchong, China

We investigated the bacterial and archaeal diversity in two hot spring microbial mats from the geothermal region of Tengchong in the Yunnan Province, China, using direct molecular analyses. The Langpu (LP) laminated mat was found by the side of a boiling pool with temperature of 60-65?°C and a pH of 8.5, while the Tengchong (TC) streamer mat consisted of white streamers in a slightly acidic (pH 6.5) hot pool outflow with a temperature of 72?°C. Four 16S rRNA gene clone libraries were constructed and restriction enzyme analysis of the inserts was used to identify unique sequences and clone frequencies. From almost 200 clones screened, 55 unique sequences were retrieved. Phylogenetic analysis showed that the LP mat consisted of a diverse bacterial population [Cyanobacteria, Chloroflexi, Chlorobia, Nitrospirae, 'Deinococcus-Thermus', Proteobacteria (alpha, beta and delta subdivisions), Firmicutes, Bacteroidetes and Actinobacteria], while the archaeal population was dominated by methanogenic Euryarchaeota and Crenarchaeota. In contrast, the TC streamer mat consisted of a bacterial population dominated by Aquificae, while the archaeal population also contained Korarchaeota as well as Crenarchaeota and methanogenic Euryarchaeota. These mats harboured clone sequences affiliated to unidentified lineages, suggesting that they are a potential source for discovering novel bacteria and archaea.     

Variation in archaeal and bacterial community profiles and their functional metabolic predictions under the influence of pure and mixed fertilizers in paddy soil

Impact of environmental perturbations i.e., nitrogen (N), phosphorus (P), potassium (K), and rice straw (Rs) on the dynamics of soil bacterial and archaeal communities are multifactor dependent and seeks a contemporary approach to study underlying mechanisms. The current study investigates the effect of pure and mixed fertilizers on soil physicochemical properties, the microbial community structure, and their functional metabolic predictions. It involved amendments with distinct combinations of N as C(H₂N)₂O, P and K as KH₂PO₄, K as KCl, and Rs in paddy soil microcosms with concentrations common in rice fields agriculture. Soil pH, electrical conductivity (EC), total carbon (TC), total nitrogen (TN), organic matter (OM), available K (AK), and total extractable P (TEP) were evaluated. To comprehend community variation and functional predictions, 16S rRNA-based high throughput sequencing (HTS) and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) were employed, respectively. Our findings showed enhanced community richness and diversity in all amendments compared to control. Proteobacteria, Actinobacteria, and Firmicutes were dominant bacterial phyla. Regarding relative abundance, Chloroflexi, Bacteroidetes, and Verrucomicrobia showed positive while Actinobacteria, Acidobacteria, and Gemmatimonadetes showed negative trends compared to controls. Thaumarchaeota and Euryarchaeota were dominant archaeal phyla and exhibited increasing and decreasing trends, respectively. The PICRUSt analysis indicated functional prediction more towards amino acid, carbohydrate, energy, and lipid metabolism while less towards others. Concerning energy metabolism, most and least responsive treatments were KP and controls, respectively. These outcomes enhanced our understanding regarding soil quality, fertilizer composition and application, and functional metabolomics of archaea and bacteria.     

Real-time PCR quantification of the predominant bacterial divisions in the distal gut of Meishan and Landrace pigs

Firmicutes and Bacteroidetes are closely related to body fat in humans and mice, which are the two dominant bacterial divisions of gut microbiota in mammals. Here real-time PCR analysis indicated that Meishan pigs had a 34% reduction in percentage Bacteroidetes (P=0.008) and a significantly lower proportion of Bacteroides (P=0.013) than Landrace pigs. The percentage of Bacteroidetes or Bacteroides had a negative correlation with body fat (R(2) was 0.63 for Bacteroidetes and 0.57 for Bacteroides, P<0.05). There was a trend that the percentage of Firmicutes in Meishan pigs was higher in numerical value than in Landrace pigs, although this difference was not statistically significant (P=0.290) between the two breeds. These suggested that body fat correlated with the percentage of Bacteroidetes division of the gut microbiota in the common pig breeds, and the differences of gut microbial ecology in obese versus lean animals may be analogous.     

Microbial communities from methane hydrate-bearing deep marine sediments in a forearc basin

Microbial communities in cores obtained from methane hydrate-bearing deep marine sediments (down to more than 300 m below the seafloor) in the forearc basin of the Nankai Trough near Japan were characterized with cultivation-dependent and -independent techniques. Acridine orange direct count data indicated that cell numbers generally decreased with sediment depth. Lipid biomarker analyses indicated the presence of viable biomass at concentrations greater than previously reported for terrestrial subsurface environments at similar depths. Archaeal lipids were more abundant than bacterial lipids. Methane was produced from both acetate and hydrogen in enrichments inoculated with sediment from all depths evaluated, at both 10 and 35 degrees C. Characterization of 16S rRNA genes amplified from the sediments indicated that archaeal clones could be discretely grouped within the Euryarchaeota and Crenarchaeota domains. The bacterial clones exhibited greater overall diversity than the archaeal clones, with sequences related to the Bacteroidetes, Planctomycetes, Actinobacteria, Proteobacteria, and green nonsulfur groups. The majority of the bacterial clones were either members of a novel lineage or most closely related to uncultured clones. The results of these analyses suggest that the microbial community in this environment is distinct from those in previously characterized methane hydrate-bearing sediments.