Bacterial 16S rRNA Gene Copies Research Articles

Factors determining microbial colonization of liquid nitrogen storage tanks used for archiving biological samples

The availability of bioresources is a precondition for life science research, medical applications, and diagnostics, but requires a dedicated quality management to guarantee reliable and safe storage. Anecdotal reports of bacterial isolates and sample contamination indicate that organisms may persist in liquid nitrogen (LN) storage tanks. To evaluate the safety status of cryocollections, we systematically screened organisms in the LN phase and in ice layers covering inner surfaces of storage tanks maintained in different biobanking facilities. We applied a culture-independent approach combining cell detection by epifluorescence microscopy with the amplification of group-specific marker genes and high-throughput sequencing of bacterial ribosomal genes. In the LN phase, neither cells nor bacterial 16S rRNA gene copy numbers were detectable (detection limit, 102 cells per ml, 103 gene copies per ml). In several cases, small numbers of bacteria of up to 104 cells per ml and up to 106 gene copies per ml, as well as Mycoplasma, or fungi were detected in the ice phase formed underneath the lids or accumulated at the bottom. The bacteria most likely originated from the stored materials themselves (Elizabethingia, Janthibacterium), the technical environment (Pseudomonas, Acinetobacter, Methylobacterium), or the human microbiome (Bacteroides, Streptococcus, Staphylococcus). In single cases, bacteria, Mycoplasma, fungi, and human cells were detected in the debris at the bottom of the storage tanks. In conclusion, the limited microbial load of the ice phase and in the debris of storage tanks can be effectively avoided by minimizing ice formation and by employing hermetically sealed sample containers.

Variations in bacterial community during bioclogging in Managed Aquifer Recharge (MAR): A laboratory study

Understanding evolution of bacterial community diversity, composition, and structure is of great importance for targeted prophylaxis and treatment of bioclogging of reclaimed water after Managed Aquifer Recharge (MAR). Based on laboratory percolation experiments, temporal variations in bacterial 16S rRNA gene copy number and community diversity, composition, and structure were investigated using real-time quantitative polymerase chain reaction (qPCR) and high-throughput sequencing in this study. During the percolation experiments, the relative saturated hydraulic conductivity (Ks') decreased from 1.0 to 0.011 at 588.3 h, indicating that a complete clogging occurred in the sand columns. Correspondingly, the bacterial 16S rRNA gene copy numbers reached a maximum of 3.9 × 109 copies per gram of sand at 180.5 h, and then decreased to 6.2 × 108 copies per gram of sand at the end of the test. Four microbial samples were collected in situ from the reclaimed water (SRW), and the clogged sand columns, namely SK0.52, SK0.08 and SK0.011, of which the Ks’ values decreased to 0.52, 0.08 and 0.011, respectively. The Chao richness index values of the bacterial community were 352, 207, 205, and 197 for SRW, SK0.52, SK0.08, and SK0.011, respectively, revealing lower species richness in the sand columns. The Shannon index values were 3.27, 2.84, 3.51, and 3.21 for SRW, SK0.52, SK0.08, and SK0.011, respectively. Meanwhile, the Evenness index values were 0.56, 0.54, 0.67, and 0.61 for the four samples in turn. This result implied that the changes in bacterial diversity and evenness were not obvious. The principal coordinate analysis (PCoA) results showed major differences in bacterial community composition between the four samples. A variety of bacterial phyla were found, among which Proteobacteria were predominant. For the non-Proteobacterial phyla, Parcubacteria, Acidobacteria, Chlamydiae, Gracilibacteria, Chloroflexi, and Saccharibacteria disappeared when moving from the raw reclaimed water to the solid porous media. Instead, Bacteroidetes and Actinobacteria were detected in the sand samples. Although some differences existed, a core group of bacteria persisted and might play a critical role during MAR bioclogging.

Evaluating the response of anaerobic ammonium-oxidizing bacteria to heavy metal spill in freshwater sediment.

Anaerobic ammonium-oxidizing (anammox) bacteria can play an important role in nitrogen elimination in the environment. However, the effect of heavy metals on anammox bacteria in aquatic ecosystem remains largely unknown. The present study investigated the variability of anammox bacterial community in a freshwater reservoir after a severe heavy metal spill. The richness (Chao1 richness estimator = 2-18), diversity (Shannon index = 0.26-2.04) and community structure of anammox bacteria changed considerably with sampling date, while anammox bacterial abundance (from 1.38 × 105 to 3.09 × 105 anammox bacterial 16S rRNA gene copies per gram dry sediment) was less responsive to metal spill. Anammox bacterial communities were mainly composed of Brocadia- and Anammoxoglobus-like bacteria as well as novel phylotype, however, there relative abundance varied among sampling dates. This work could add the knowledge of the response of anammox bacteria to heavy metal contamination.

Oil degradation potential of microbial communities in water and sediment of Baltic Sea coastal area.

Two long-term potentially oil exposed Baltic Sea coastal sites near old oil refineries and harbours were compared to nearby less exposed sites in terms of bacterial, archaeal and fungal microbiomes and oil degradation potential. The bacterial, archaeal and fungal diversities were similar in oil exposed and less exposed sampling sites based on bacterial and archaeal 16S rRNA gene and fungal 5.8S rRNA gene amplicon sequencing from both DNA and RNA fractions. The number of genes participating in alkane degradation (alkB) or PAH-ring hydroxylation (PAH–RHDα) were detected by qPCR in all water and sediment samples. These numbers correlated with the number of bacterial 16S rRNA gene copies in sediment samples but not with the concentration of petroleum hydrocarbons or PAHs. This indicates that both the clean and the more polluted sites at the Baltic Sea coastal areas have a potential for petroleum hydrocarbon degradation. The active community (based on RNA) of the coastal Baltic Sea water differed largely from the total community (based on DNA). The most noticeable difference was seen in the bacterial community in the water samples were the active community was dominated by Cyanobacteria and Proteobacteria whereas in total bacterial community Actinobacteria was the most abundant phylum. The abundance, richness and diversity of Fungi present in water and sediment samples was in general lower than that of Bacteria and Archaea. Furthermore, the sampling location influenced the fungal community composition, whereas the bacterial and archaeal communities were not influenced. This may indicate that the fungal species that are adapted to the Baltic Sea environments are few and that Fungi are potentially more vulnerable to or affected by the Baltic Sea conditions than Bacteria and Archaea.

Production of Dibromomethane and Changes in the Bacterial Community in Bromoform-Enriched Seawater.

The responses of bacterial communities to halocarbon were examined using a 28-d incubation of bromoform- and methanol-enriched subarctic surface seawater. Significant increases were observed in dibromomethane concentrations and bacterial 16S rRNA gene copy numbers in the treated substrates incubated for 13 d. The accumulated bacterial community was investigated by denaturing gradient gel electrophoresis and amplicon analyses. The dominant genotypes corresponded to the genera Roseobacter, Lentibacter, and Amylibacter; the family Flavobacteriaceae; and the phylum Planctomycetes, including methylotrophs of the genus Methylophaga and the family Methylophilaceae. Therefore, various phylotypes responded along with the dehalogenation processes in subarctic seawater.

Changes in soil microbial community response to precipitation events in a semi-arid steppe of the Xilin River Basin, China

In the context of climate change, precipitation is predicted to become more intense at the global scale. Such change may alter soil microbial communities and the microbially mediated carbon and nitrogen dynamics. In this study, we experimentally repackaged precipitation patterns during the growing season (from June to September) of 2012 in a semi-arid temperate steppe of the Xilin River Basin in Inner Mongolia of China, based on the 60-year growing season precipitation data. Specifically, a total amount of 240 mm simulated precipitation was assigned to experimental plots by taking the following treatments: (1) P6 (6 extreme precipitation events, near the 1st percentile); (2) P10 (10 extreme precipitation events, near the 5th percentile); (3) P16 (16 moderate precipitation events, near the 50th percentile); and (4) P24 (24 events, 60-year average precipitation, near the 50th percentile). At the end of the growing season, we analyzed soil microbial community structure and biomass, bacterial abundance, fungal abundance and bacterial composition, by using phospholipid fatty acid (PLFA), real-time quantitative polymerase chain reaction (RT-qPCR) and 16S rRNA gene clone library methods. The extreme precipitation events did not change soil microbial community structure (represented by the ratio of PLFA concentration in fungi to PLFA concentration in bacteria, and the ratio of PLFA concentration in gram-positive bacterial biomass to PLFA concentration in gram-negative bacterial biomass). However, the extreme precipitation events significantly increased soil microbial activity (represented by soil microbial biomass nitrogen and soil bacterial 16S rRNA gene copy numbers). Soil fungal community showed no significant response to precipitation events. According to the redundancy analysis, both soil microbial biomass nitrogen and soil ammonium nitrogen (NH4-N) were found to be significant in shaping soil microbial community. Acidobacteria, Actinobacteria and Proteobacteria were the dominant phyla in soil bacterial composition, and responded differently to the extreme precipitation events. Based on the results, we concluded that the extreme precipitation events altered the overall soil microbial activity, but did not impact how the processes would occur, since soil microbial community structure remained unchanged.

Influence of Heat Events on the Composition of Airborne Bacterial Communities in Urban Ecosystems.

Airborne bacteria are significantly affected by meteorological and environmental conditions. However, there is little quantitative data available on the effects of these factors on airborne bacteria in urban ecosystems. In the present study, we analyzed weather-dependent changes in the composition of airborne bacterial communities using high throughput sequencing. Samples were collected before and after a period of constant hot weather at four selected sampling sites (YRBS, ZJGUSJC, TJCR, and BLQG) in Hangzhou. Our results show that the average amount of bacterial 16S rRNA gene copy numbers per m3 of air decreased significantly after constant high temperature. In addition, the number of operational taxonomic units and the Shannon–Wiener diversity indexes of the samples at all four selected sampling sites were significantly decreased after the heat event, showing notable impact on bacterial diversity. We also detected a significant increase in the abundances of spore-forming bacteria. Firmicutes increased from 3.7% to 9.9%, Bacillales increased from 2.6% to 7.6%, and Bacillaceae increased from 1.5% to 5.9%. In addition, we observed an increase in beta-Proteobacteria (18.2% to 50.3%), Rhodocyclaceae (6.9% to 29.9%), and Burkholderiaceae (8.1% to 15.2%). On the other hand, the abundance of alpha-Proteobacteria (39.6% to 9.8%), Caulobacteraceae (17.9% to 0.5%), Sphingomonadaceae (7.2% to 3.3%), and Xanthomonadaceae (3.0% to 0.5%) was significantly lower. Taken together, our data suggest that the composition of airborne bacterial communities varies greatly dependent on heat events, and that such communities include several species that are highly susceptible to high-temperature related stressors such as high air temperature, low relative humidity, and high intensity of solar radiation.

Alterations in the Abundance and Co-occurrence of Akkermansia muciniphila and Faecalibacterium prausnitzii in the Colonic Mucosa of Inflammatory Bowel Disease Subjects.

Akkermansia muciniphila and Faecalibacterium prausnitzii, cohabitants in the intestinal mucosa, are considered members of a healthy microbiota and reduction of both species occurs in several intestinal disorders, including inflammatory bowel disease. Little is known however about a possible link between the reduction in quantity of these species, and in which circumstances this may occur. This study aims to determine the abundances and co-occurrence of the two species in order to elucidate conditions that may compromise their presence in the gut. Loads of A. muciniphila, total F. prausnitzii and its two phylogroup (16S rRNA gene copies) were determined by quantitative polymerase chain reaction in colonic biopsies from 17 healthy controls (H), 23 patients with ulcerative colitis (UC), 31 patients with Crohn's disease (CD), 3 with irritable bowel syndrome (IBS) and 3 with colorectal cancer (CRC). Data were normalized to total bacterial 16S rRNA gene copies in the same sample. Prevalence, relative abundances and correlation analyses were performed according to type of disease and considering relevant clinical characteristics of patients such as IBD location, age of disease onset, CD behavior, current medication and activity status. Co-occurrence of both species was found in 29% of H, 65% of UC and 29% of CD. Lower levels of total F. prausnitzii and phylogroups were found in subjects with CD, compared with H subjects (P ≤ 0.044). In contrast, no differences were found with the regard to A. muciniphila abundance across different disease states, but CD patients with disease onset below 16 years of age featured a marked depletion of this species. In CD patients, correlation between A. muciniphila and total F. prausnitzii (ρ = 0.362, P = 0.045) was observed, and particularly in those with non-stricturing, non-penetrating disease behavior and under moderate immunosuppressants therapy. Altogether, this study revealed that co-occurrence of both species differs between disease status. In addition, IBD patients featured a reduction of F. prausnitzii but similar loads of A. muciniphila when compared to H subjects, with the exception of those with early onset CD. Depletion of A. muciniphila in this subgroup of subjects suggests that it could be a potential biomarker to assist in pediatric CD diagnosis.

AB100. P074. Novel biomarkers for differential diagnosis of intraductal papillary mucinous neoplasms revealed by profiling microbial composition and translocation markers in liquid biopsies

: Pancreatic ductal adenocarcinoma (PDAC) has a major impact on public health, being the fourth-leading cause of cancer-related death in Western countries with a low overall survival rate and rapid deterioration in quality of life. Intraductal papillary mucinous neoplasms (IPMNs) are neoplastic precursor lesions which are understood to evolve from lesions with low-grade dysplasia to high-grade dysplasia to PDAC. Currently, the accuracy of pre-surgery differential diagnosis of cystic lesions is merely 47–78%. However, only after surgical resection of the pancreas can the type of cystic neoplasms and degree of IPMN dysplasia accurately be determined. The discovery of novel biomarkers that improve timely and accurate diagnosis of IPMN and its grade of dysplasia, and thus assist the determination of health risk, are of great importance for better patient management and to minimize diagnostic errors and unnecessary surgical procedures. We hypothesize that gut microbiota may have a role on pancreatic tumorogenesis and progression, given the strong association of oral pathogens such as P. gingivalis and F. nucleatum with systemic inflammation and intestinal cancers. We aimed to (I) determine whether (oral) bacteria are present in pancreatic cystic lesions, and (II) whether cystic microbiota composition associates with IPMN disease severity. We have established a biobank of pancreatic cyst fluid and peripheral blood from patients with pancreatic cystic lesions (n=90, IPMN and benign neoplasms as control) with post-surgery validated diagnosis. The absolute bacterial 16S rRNA gene copy numbers were determined by TaqMan qPCR and microbial compositional profiling by 16S rRNA gene sequencing is being undertaken. Additionally, we measured the magnitude of microbial translocation (MT) inflammation markers in these samples. We found a statistically significant difference of bacterial 16S gene quantities as well as biomarkers of MT and inflammation between different types of pancreatic cystic lesions, as well as significant correlation with IPMN grade of dysplasia. Our finding that several novel biomarkers from liquid biopsies might be used to differentiate between benign and (pre-)malignant pancreatic cystic lesions is of important clinical relevance in diagnosis and treatment for IPMN-related morbidity and mortality, including PDAC.

Green tea extract and black tea extract differentially influence cecal levels of short-chain fatty acids in rats.

Increasing evidence indicates that gut microbiota plays a critical role to maintain the host's health. The biological function of microbially produced short‐chain fatty acids (SCFA) becomes the focus of attention. This study aimed to compare the effects of green tea extract (GTE) and black tea extract (BTE) on cecal levels of SCFA in rats. Rats consumed an assigned diet of either a control diet, a GTE diet (10 g/kg), or a BTE diet (10 g/kg), for 3 weeks. The dietary addition of GTE significantly reduced the concentrations of acetate and butyrate in cecal digesta compared to the control, but BTE showed an increased trend for a cecal pool. In the GTE group, a significant amount of undigested starch was excreted in feces, but BTE produced no effect. Interestingly, feces of rats fed the BTE diet contained higher bacterial 16S rRNA gene copy numbers for total eubacteria compared to the control diet. Taken together, treatments of the diets with GTE and BTE brought about a different degree of producing SCFA in rat cecum. BTE might advantageously stimulate more SCFA production than GTE by facilitating bacterial utilization of starch.

Comparative analyses of microbial structures and gene copy numbers in the anaerobic digestion of various types of sewage sludge

Anaerobic co-digestion of various sewage sludges is a promising approach for greater recovery of energy, but the process is more complicated than mono-digestion of sewage sludge. The applicability of microbial structure analyses and gene quantification to understand microbial conditions was evaluated. The results show that information from gene analyses is useful in managing anaerobic co-digestion and damaged microbes in addition to conventional parameters like total solids, pH and biogas production. Total bacterial 16S rRNA gene copy numbers are the most useful tools for evaluating unstable anaerobic digestion of sewage sludge, rather than mcrA and total archaeal 16S rRNA gene copy numbers, and high-throughput sequencing. First order decay rates of gene copy numbers during pH failure were higher than typical decay rates of microbes in stable operation. The sequencing analyses, including multidimensional scaling, showed very different microbial structure shifts, but the results were not consistent.

An in vitro study to assess the impact of tetracycline on the human intestinal microbiome

The human intestinal microbiome, a generally stable ecosystem, could be potentially altered by the ingestion of antimicrobial drug residues in foods derived from animals. Data and the scientific published literature on the effects of antimicrobial residues on the human intestinal microbiome are reviewed by national regulatory authorities as part of the human food safety evaluation of veterinary antimicrobial agents used in food-producing animals. In this study, we determined if tetracycline, at low residue concentrations, could impact the human intestinal microbiome structure and the resistance-gene profile, following acute and subchronic exposure. The effects of 0.15, 1.5, 15, and 150 μg/ml of tetracycline, after 24 h and 40 days of exposure, in 3% human fecal suspensions, collected from three individuals (A, B, and C) were investigated using in vitro batch cultures. Results were variable, with either no change or minor changes in total bacterial 16S rRNA gene copies after exposure of fecal samples to tetracycline, because of the inter-individual variation of human gastrointestinal tract microbiota. Bacterial community analysis using rRNA-based pyrosequencing revealed that Firmicutes and Bacteroidetes were the predominant phyla in the three fecal samples; the ratio of phylotypes varied among individuals. The evaluation of bacterial community changes at the genus level, from control to tetracycline-treated fecal samples, suggested that tetracycline under the conditions of this study could lead to slight differences in the composition of intestinal microbiota. The genus Bacteroides (of the Bacteroidetes) was consistently altered from 1.68 to 5.70% and 4.82–8.22% at tetracycline concentrations of 0.15 μg/ml or above at both time points for individual A, respectively, and increased 5.13–13.50% and 10.92–22.18% for individual B, respectively. Clostridium family XI increased 3.50–25.34% in the presence of tetracycline at 40 days for individual C. Principal Component Analysis (PCA) confirmed the pyrosequencing findings of inter-individual variability of the ratio of phylotypes and the effect of tetracycline. Among the 23 tetracycline resistance genes (TRGs) screened, four tet genes (tetO, Q, W, and X) were major TRGs in control and tetracycline-dosed fecal samples. A variable to slight increase of copy number of TRGs appeared to be related to tetracycline treatment, interindividual variability and duration of exposure. Despite, the inherent variability of the intestinal microbiota observed among or within individuals, this pilot study contributes to the knowledge base of the impact of low residue concentrations of tetracycline on the human intestinal microbiome on the potential for antimicrobial resistance.

Rhizoremediation of a dioxin-like PCB polluted soil by alfalfa: Dynamic characterization at temporal and spatial scale

This study investigates the temporal and spacial dissipation dynamics of a dioxin-like polychlorinated biphenyl (PCB 77) in the rhizosphere of alfalfa. A three-chamber rhizobox was designed to compare the PCB 77 dissipation efficiency in the rhizosphere, near-rhizosphere, and far-rhizosphere zones. Culture-independent techniques, including quantitative PCR (qPCR), Biolog-ECO plate, and denatured gradient gel electrophoresis (DGGE) were employed to investigate the variation of bacterial quantity, metabolic diversity and community structure in the alfalfa-rhizobium symbiosis rhizosphere at different rhizoremediation stages. PCB dissipation rates in different rhizosphere zones were in the order: rhizosphere (90.9%) > near-rhizosphere (80.5%) > far-rhizosphere (31.7%). The number of the bacterial 16S rRNA gene copies in the rhizosphere zone in the polluted treatment reached the highest value of all the treatments. Microbial metabolic diversity, as indicated by average well color development (AWCD) in both rhizosphere and near-rhizosphere zones, had recovered from the PCB 77 pollution. The soil bacterial community diversity improved greatly in the rhizosphere of alfalfa, with some new species appeared in the rhizosphere and near-rhizosphere zones. In conclusion, the dissipation of PCB 77, the quantity of total soil bacteria, soil microbial metabolic diversity, and soil microbial community structure were significantly improved in rhizosphere and near-rhizosphere zones of alfalfa.

High level bacterial contamination of secondary school students' mobile phones.

While contamination of mobile phones in the hospital has been found to be common in several studies, little information about bacterial abundance on phones used in the community is available. Our aim was to quantitatively determine the bacterial contamination of secondary school students' mobile phones. Altogether 27 mobile phones were studied. The contact plate method and microbial identification using MALDI-TOF mass spectrometer were used for culture studies. Quantitative PCR reaction for detection of universal 16S rRNA, Enterococcus faecalis 16S rRNA and Escherichia coli allantoin permease were performed, and the presence of tetracycline (tetA, tetB, tetM), erythromycin (ermB) and sulphonamide (sul1) resistance genes was assessed. We found a high median bacterial count on secondary school students' mobile phones (10.5 CFU/cm2) and a median of 17,032 bacterial 16S rRNA gene copies per phone. Potentially pathogenic microbes (Staphylococcus aureus, Acinetobacter spp., Pseudomonas spp., Bacillus cereus and Neisseria flavescens) were found among dominant microbes more often on phones with higher percentage of E. faecalis in total bacterial 16S rRNA. No differences in contamination level or dominating bacterial species between phone owner's gender and between phone types (touch screen/keypad) were found. No antibiotic resistance genes were detected on mobile phone surfaces. Quantitative study methods revealed high level bacterial contamination of secondary school students' mobile phones.

Influence of land use on bacterial and archaeal diversity and community structures in three natural ecosystems and one agricultural soil.

Studying shifts in microbial communities under different land use can help in determining the impact of land use on microbial diversity. In this study, we analyzed four different land-use types to determine their bacterial and archaeal diversity and abundance. Three natural ecosystems, that is, wetland (WL), grassland (GL), and forest (FR) soils, and one agricultural soil, that is, tea plantation (TP) soil, were investigated to determine how land use shapes bacterial and archaeal diversity. For this purpose, molecular analyses, such as quantitative polymerase chain reaction (Q-PCR), 16S rRNA gene sequencing, and terminal restriction fragment length polymorphism (T-RFLP), were used. Soil physicochemical properties were determined, and statistical analyses were performed to identify the key factors affecting microbial diversity in these soils. Phylogenetic affiliations determined using the Ribosomal Database Project (RDP) database and T-RFLP revealed that the soils had differing bacterial diversity. WL soil was rich in only Proteobacteria, whereas GR soil was rich in Proteobacteria, followed by Actinobacteria. FR soil had higher abundance of Chloroflexi species than these soils. TP soil was rich in Actinobacteria, followed by Chloroflexi, Acidobacteria, Proteobacteria, and Firmicutes. The archaeal diversity of GL and FR soils was similar in that most of their sequences were closely related to Nitrososphaerales (Thaumarchaeota phylum). In contrast, WL soil, followed by TP soil, had greater archaeal diversity than other soils. Eight different archaeal classes were found in WL soil, and Pacearchaeota class was the richest one. The abundance of bacterial and archaeal 16S rRNA gene copies in WL and GL soils was significantly higher than that in FR and TP soils. Redundancy analysis showed that bacterial diversity was influenced by abiotic factors, e.g., total organic carbon and pH, whereas total nitrogen, pH, and cation exchange capacity (CEC) significantly affected archaeal community composition. Pearson correlation analysis showed that bacterial and archaeal 16S rRNA gene abundance had the highest correlation with clay content (r > 0.905, P < 0.01), followed by total-P, CEC, pH, and silt (%). These results will lead to more comprehensive understanding of how land use affects microbial distribution.

PH is the primary determinant of the bacterial community structure in agricultural soils impacted by polycyclic aromatic hydrocarbon pollution

Acidification and pollution are two major threats to agricultural ecosystems; however, microbial community responses to co-existed soil acidification and pollution remain less explored. In this study, arable soils of broad pH (4.26–8.43) and polycyclic aromatic hydrocarbon (PAH) gradients (0.18–20.68 mg kg−1) were collected from vegetable farmlands. Bacterial community characteristics including abundance, diversity and composition were revealed by quantitative PCR and high-throughput sequencing. The bacterial 16S rRNA gene copies significantly correlated with soil carbon and nitrogen contents, suggesting the control of nutrients accessibility on bacterial abundance. The bacterial diversity was strongly related to soil pH, with higher diversity in neutral samples and lower in acidic samples. Soil pH was also identified by an ordination analysis as important factor shaping bacterial community composition. The relative abundances of some dominant phyla varied along the pH gradient, and the enrichment of a few phylotypes suggested their adaptation to low pH condition. In contrast, at the current pollution level, PAH showed marginal effects on soil bacterial community. Overall, these findings suggest pH was the primary determinant of bacterial community in these arable soils, indicative of a more substantial influence of acidification than PAH pollution on bacteria driven ecological processes.

A long-term hybrid poplar plantation on cropland reduces soil organic carbon mineralization and shifts microbial community abundance and composition

Poplar plantations have been established around the world to provide timber or fuelwood and to control erosion in degraded areas. The objective of this study was to investigate the effects of converting croplands to long-term hybrid poplar (Populus×euramericana cv. I-72) plantations for 10, 15 and 20 years on soil bacterial and fungal communities and on their relationships with soil organic carbon (SOC) mineralization. Overall, the results indicated that the long-term hybrid poplar plantations increased soil pH, SOC, total N and moisture contents and decreased dissolved organic carbon (DOC), NH4+ and NO3− contents compared to that on the cropland. There were lower cumulative amounts of CO2 respired and SOC mineralization rates in the hybrid poplar plantation soils compared to that of the cropland. The hybrid poplar plantation with 20 years caused a greater fungal internal transcribed spacer (ITS) gene copy number and a lower bacterial 16S rRNA gene copy number and dehydrogenase and β-glucosidase activities compared to that in the cropland soils. As indicated by Illumina MiSeq sequencing, the establishment of hybrid poplar plantations harbored distinct soil bacterial and fungal communities, which were strongly correlated with specific soil properties. We further found that the SOC mineralization rate was positively correlated to the bacterial abundance and the relative abundances of Actinobacteria and Bacteroidetes, whereas negatively correlated to the fungal abundance. This study suggested that the long-term hybrid poplar plantation reduced SOC mineralization, causing changes in habitats that favor fungal community growth and shifts in bacterial community composition to more facultative and/or obligate anaerobes and less microbes that are capable of decomposing recalcitrant carbon, which may help enhance SOC accumulation in soil and mitigate climate change.

Soil urease activity and bacterial ureC gene copy numbers: Effect of pH

Urea-N is ubiquitous in soils, having both natural and anthropogenic sources. The enzyme urease catalyzes its hydrolysis to NH3 and is produced by plants and many soil microorganisms, but there are growing concerns related to possible urea-induced eutrophication of surface waters proximate to agricultural fields. Agronomic research has focused on the relationship between urea hydrolysis and soil physical or chemical properties, rather than on direct measurements of the microbial community and its population diversity, especially using quantification of genes that code for urease. We quantified bacterial and archaeal 16S rRNA, fungal ITS, and bacterial ureC gene copies as a function of physical and chemical soil properties. Soils were sampled from A and B horizons along a toposequence that comprised an agricultural field, a grassed field border, and a forested riparian zone in the Chesapeake Bay watershed of Maryland. The riparian zone soils contained the highest total number of genes among both A- and B-horizon soils. The soils were then experimentally altered in the laboratory to achieve a range of pH values between 3.1 and 7.1. Soil pH was chosen as a variable because it varies both naturally and due to agronomic practices, and it influences microbial community structure and function. Archaeal 16S rRNA extracted from the pH-adjusted soils did not show a consistent pattern of increase or decrease with changes in pH, while ITS was greatest at low pH and bacterial 16S and bacterial ureC were greatest at high pH. We measured higher urea hydrolysis rates and gene copy numbers in A-horizon soils than in B-horizon soils, and found that urea hydrolysis rate was significantly correlated with gene copies of bacterial 16S, ureC, and increased pH. This suggests that liming acid soils increases urea hydrolysis rates in part by encouraging the growth of microorganisms capable of producing urease.

Diversity and abundance of ammonia-oxidizing bacteria (AOB) revealed by PCR amplification of amoA gene in a polyacrylamide transportation system of an oilfield

Microorganisms were detected in the hydrolyzed high-molecular-weight polyacrylamide (HPAM) transportation system. The diversity of both general bacteria and ammonia-oxidizing bacteria (AOB) in the online distribution system was further analyzed using 16S rRNA and the functional amoA genes through PCR amplification and clone library methods together with the physicochemical properties and environmental factors of samples. In total, twenty-four families of bacteria were identified in the system; biofilm sample showed higher diversity and production water showed lower diversity than the other samples. The AOB-like phylotypes in sample S6 mainly showed high alignment to Nitrosospira briensis while others in samples showed low alignment to the known uncultrued AOB, indicative of new AOB phylotypes possibly. The abundance of AOB amoA gene abundance ranged from 3.54 × 102 to 2.04 × 103 copies·ml−1, where were significantly lower than those of bacterial 16S rRNA gene copies from 2.94 × 106 to 6.33 × 108 copies·ml−1 in samples S4–S6. The RDA analysis showed that the AOB amoA gene was positively related to the concentration of NH4+, NO2−, NO3−, SO42− and S2−. The results showed the distribution of bacterial amoA gene for nitrification in this polyacrylamide transporting system and the information enriches our knowledge of microbial community diversity in the nitrogen cycle of the polyacrylamide transportation system.

Microbial consortia controlling biogenic gas formation in the Qaidam Basin of western China

AbstractKnowledge of what controls the activity of subsurface microbial communities is critical for assessing and managing biogenic methane resources. In this study, 19 formation waters and five gas samples were collected at depths of 800 to 1900 m from Quaternary biogenic gas fields of the Qaidam Basin, China. The formation waters were brines with chloride (Cl) concentrations from 1200 to 2700 mM. Bacterial 16S rRNA gene copies ranged from 3.75 × 104 to 2.23 × 106 copies mL−1 of water, and those of archaea ranged from 2.44 × 103 to 4.66 × 107 copies mL−1 of water. Both bacterial and archaea 16 s rRNA gene copies were negatively correlated with Cl concentration. The microbial community structure differed significantly depending on Cl concentrations. At high Cl waters (&gt;1800 mM), the microbial community showed a halophilic signature made up of several abundant taxonomic groups within Firmicules, γ‐Proteobacteria, and methylotrophic Methanosarcinales. At low Cl, Firmicules and hydrogenotrophic methanogens were dominant members. The proportion of inferred hydrogenotrophic methanogens decreased from 89% to 14% of total archaeal reads with increasing Cl concentration; in contrast, methylotrophic species increased from 11% to 85%. Given that the proportion of hydrogenotrophic species was positively correlated with the archaeal gene abundances, we suggest that Cl concentrations primarily constrain the activity of archaea catalyzing H2 reduction of CO2. Our results show that dilution of formation waters is critical in the process of biogenic gas formation, suggesting that an engineered decrease in Cl concentrations may induce methanogenesis as a potential method to increase gas reserves in such areas in the future.