Abundance and Diversity of Viruses in Six Delaware Soils

The importance of viruses in marine microbial ecology has been established over the past decade. Specifically, viruses influence bacterial abundance and community composition through lysis and alter bacterial genetic diversity through transduction and lysogenic conversion. By contrast, the abundance and distribution of viruses in soils are almost completely unknown. This study describes the abundance and diversity of autochthonous viruses in six Delaware soils: two agricultural soils, two coastal plain forest soils, and two piedmont forest soils. Viral abundance was measured using epifluorescence microscopy, while viral diversity was assessed from morphological data obtained through transmission electron microscopy. Extracted soil virus communities were dominated by bacteriophages that demonstrated a wide range of capsid diameters (20 nm to 160 nm) and morphologies, including filamentous forms and phages with elongated capsids. The reciprocal Simpson's index suggests that forest soils harbor more diverse assemblages of viruses, particularly in terms of morphological distribution. Repeated extractions of virus-like particles (VLPs) from soils indicated that the initial round of extraction removes approximately 70% of extractable viruses. Higher VLP abundances were observed in forest soils (1.31 × 10⁹ to 4.17 × 10⁹ g⁻¹ dry weight) than in agricultural soils (8.7 × 10⁸ to 1.1 × 10⁹ g⁻¹ dry weight). Soil VLP abundance was significantly correlated to moisture content (r = 0.988) but not to soil texture. Land use (agricultural or forested) was significantly correlated to both bacterial (r = 0.885) and viral (r = 0.812) abundances, as were soil organic matter and water content. Thus, land use is a significant factor influencing viral abundance and diversity in soils.     

Diversity and Abundance of Ammonia-Oxidizing Archaea and Bacteria in Diverse Chinese Paddy Soils

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) in three types of paddy soils of China before and after rice plantation were investigated by using an integrated approach including geochemistry, 454 pyrosequencing, and quantitative polymerase chain reaction (PCR). The abundances of AOA amoA gene were 1～2 orders of magnitude higher than AOB amoA gene. The types of paddy soils had important impacts on the diversities of both AOA and AOB via clay mineralogy (smectite or illite-rich) and bioavailability of ammonium. The Nitrososphaera subcluster 5 and Nitrosopumilis cluster of AOA, and Nitrosomonas subcluster 5 and Nitrosospira subcluster 3 of AOB were well adapted to soils with high ammonium concentrations. AOA and AOB community structures were different before and after rice plantation, likely due to changes of pH and ammonium fertilization. The Nitrosospira subclusters 2 and 9 were well adapted to acidic paddy soils. However, the sensitivity of AOA and AOB community structures to these factors may be complicated by other geochemical conditions. The results of this study collectively demonstrated that multiple environmental factors, such as clay mineralogy, ammonium content and total organic carbon as well as soil pH, shaped AOA and AOB community structure and abundance.     

Diversity of thermophilic and non-thermophilic Crenarchaeota at 80 degrees C

A hot spring in the solfataric field of Pisciarelli (Naples-Italy) was analysed for Archaeal diversity. Total DNA was extracted from the environment, archaeal 16S rRNA genes were amplified with Archaea specific primers, and a clone library consisting of 201 clones was established. The clones were grouped in 10 different groups each representing a specific band pattern using restriction fragment length polymorphism (RFLP). Members of all 10 groups were sequenced and phylogenetically analyzed. Surprisingly, a high abundance of clones belonging to non-thermophilic Crenarchaeal clusters were detected together with the thermophilic archaeon Acidianus infernus in this thermophilic environment. Neither Sulfolobus species nor other hyperthermophilic Crenarchaeota were detected in the clone library. The relative abundance of the sequenced clones was confirmed by terminal restriction fragment analyses. Amplification of 16S rRNA genes from Archaea transferred from the surrounding environment was considered negligible because DNA from non-thermophilic Crenarchaeota incubated under conditions similar to the solfatara could not be PCR amplified after 5 min.     

Genetic Diversity and Abundance of Flavobacterial Proteorhodopsin in China Seas

Proteorhodopsin (PR) genes related to Flavobacteria were found to be highly diverse in the East and South China seas and displayed a distinct geographic pattern, which appeared to reflect cold versus warm adaptation when Global Oceanic Sampling database metagenomic data were included. Flavobacterial PR genes were more abundant offshore than nearshore, implying that inheritance of the PR gene could be important for Flavobacteria living in the oligotrophic environment.     

Abundance and Diversity of Sulfate-Reducing Bacteria in High Arsenic Shallow Aquifers

The abundance, diversity, and relative distribution of sulfate-reducing bacteria (SRB) in high arsenic (As) groundwater aquifers of Hangjinhouqi County in the Hetao Basin, Inner Mongolia was investigated using denaturing gradient gel electrophoresis (DGGE) and quantitative polymerase chain reaction (qPCR) analysis of dsrB genes (encoding dissimilatory sulfite reductase beta-subunit). DGGE results revealed that SRB populations were diverse, but were mainly composed of Desulfotomaculum, Desulfobulbus, Desulfosarcina, and Desulfobacca. The abundance of Desulfobulbus was positively correlated with the ratio of Fe(II)/Fe(III). Although qPCR results showed that the dsrB gene abundance in groundwater samples ranged from below detection to 4.9 × 10⁶ copies/L, and the highest percentage of dsrB gene copies to bacterial 16S rRNA gene copies was 2.1%. Geochemical analyses showed that As(III) content and the ratio of Fe(II) to Fe(III) increased with total As, while sulfate concentrations decreased. Interestingly, the dsrB gene abundance was positively correlated with As concentrations. These results indicate that sulfate reduction occurs simultaneously with As and Fe reduction, and might result in increased As release and mobilization when As is not incorporated into iron sulfides. This study improves our understanding of SRB and As cycling in high As groundwater systems.     

Phylogenetic Analysis of Nonthermophilic Members of the Kingdom Crenarchaeota and Their Diversity and Abundance in Soils

Within the last several years, molecular techniques have uncovered numerous 16S rRNA gene (rDNA) sequences which represent a unique and globally distributed lineage of the kingdom Crenarchaeota that is phylogenetically distinct from currently characterized crenarchaeotal species. rDNA sequences of members of this novel crenarchaeotal group have been recovered from low- to moderate-temperature environments (−1.5 to 32°C), in contrast to the high-temperature environments (temperature, >80°C) required for growth of the currently recognized crenarchaeotal species. We determined the diversity and abundance of the nonthermophilic members of the Crenarchaeota in soil samples taken from cultivated and uncultivated fields located at the Kellogg Biological Station’s Long-Term Ecological Research site (Hickory Corners, Mich.). Clones were generated from 16S rDNA that was amplified by using broad-specificity archaeal PCR primers. Twelve crenarchaeotal sequences were identified, and the phylogenetic relationships between these sequences and previously described crenarchaeotal 16S rDNA sequences were determined. Phylogenetic analyses included nonthermophilic crenarchaeotal sequences found in public databases and revealed that the nonthermophilic Crenarchaeota group is composed of at least four distinct phylogenetic clusters. A 16S rRNA-targeted oligonucleotide probe specific for all known nonthermophilic crenarchaeotal sequences was designed and used to determine their abundance in soil samples. The nonthermophilic Crenarchaeota accounted for as much as 1.42% ± 0.42% of the 16S rRNA in the soils analyzed.     

The Dynamic Change of Microbial Communities in Crude Oil-Contaminated Soils from Oil Fields in China

To study the biodegradability of microbial communities in crude oil contamination, crude oil-contaminated soil samples from different areas of China were collected. Using polyphasic approach, this study explored the dynamic change of the microbial communities during natural accumulation in oil field and how the constructed bioremediation systems reshape the composition of microbial communities. The abundance of oil-degrading microbes was highest when oil content was 3–8%. This oil content is potentially optimal for oil degrading bacteria proliferation. During a ～12 months natural accumulation, the quantity of oil-degrading microbes increased from 10⁵ to 10⁸ cells/g of soil. A typical sample of Liaohe (LH, oil-contaminated site near Liaohe River, Liaoning Province, China) was remediated for 50 days to investigate the dynamic change of microbial communities. The average FDA (a fluorescein diacetate approach) activities reached 0.25 abs/hr·g dry soil in the artificially enhanced repair system, 32% higher than the 0.19 abs/hr·g dry soil in natural circumstances. The abundance of oil-degrading microbes increased steadily from 0.001 to 0.068. During remediation treatment, oil content in the soil sample was reduced from 6.0% to 3.7%. GC–MS analysis indicated up to 67% utilization of C₁₀–C₂₀ normal paraffin hydrocarbons, the typical compounds that undergo microbial degradation.     

Abundance and Diversity of Sulfur-Oxidizing Bacteria along a Salinity Gradient in Four Qinghai-Tibetan Lakes,China

Sulfur-oxidizing bacteria (SOB) play important roles in the sulfur cycle and are widespread in a number of environments, but their occurrence and relationship to geochemical conditions in (hyper)saline lakes are still poorly understood. In this study, the abundance and diversity of SOB populations were investigated in four Qinghai-Tibetan lakes (Erhai Lake, Gahai Lake 1, Gahai Lake 2 and Xiaochaidan Lake) by using quantitative polymerase chain reaction (qPCR) and soxB gene- (encoding sulfate thiohydrolase) based phylogenectic analyses. qPCR analyses showed that in the studied lakes, the total bacterial 16S rRNA and soxB gene abundances in the sediments were distinctly higher than in the overlying waters. The 16S rRNA gene abundance in the waters ranged 5.27 × 10⁶–6.09 × 10⁸ copies per mL and 7.39 × 10¹⁰–2.9 × 10¹¹ copies per gram sediment. The soxB gene abundance in the waters ranged from 1.88 × 10⁴ to 5.21 × 10⁵ per mL and 4.73 × 10⁶–2.65 × 10⁷ copies per gram sediment. The soxB gene in the waters of the two hypersaline lakes (Gahai Lake 2 and Xiaochaidan Lake) was more abundant (2.97 × 10⁵ and 5.21 × 10⁵ copies per mL) than that in the two low-salinity lakes (1.88 × 10⁴ and 3.36 × 10⁴ copies per mL). Phylogenetic analysis showed that Alpha- and Betaproteobacteria were dominant SOB in the investigated lakes, and the composition of proteobacterial subgroups varied with salinity: in freshwater Erhai Lake and low-salinity Gahai Lake 1, the SOB populations were dominated by the Betaproteobacteria, whereas in hypersaline Lake Gahai 2 and Xiaochaidan Lake, the SOB populations were dominated by Alphaproteobacteria. Overall, salinity played a key role in controlling the diversity and distribution of SOB populations in the investigated Qinghai-Tibetan lakes.     

油藏水样细菌群落16S rRNA基因的RFLP分析

通过16S rRNA基因的限制性酶切片段长度多态性分析(RFLP)方法,考察了油藏水样中细菌群落及多样性。从水样中分离纯化微生物总DNA,选择性扩增细菌16S rRNA基因,并构建16S rDNA克隆文库。337个16S rDNA克隆片段分别用限制性内切酶HinfⅠ和HaeⅢ酶切分析,得到74个操作分类单元(OTUs),其中数量最多的4个OTUs共占克隆子总数的73.6%,另外70个OTUs的丰度均处于较低水平,有57个OTUs仅含有1个克隆子。结果表明,运用RFLP方法分析16S rDNA克隆片段能够有效评估油藏水样中的细菌群落和多样性。     

Cladocera Diversity,Abundance and Habitat in a Western Thailand Stream

Longitudinal and temporal distribution was determined for 40 species of cladocerans at sites between the headwaters and mouth of Khayeng Stream, a relatively pristine waterway in western Thailand. Cladocerans were confined mostly to lentic areas and abundance between April and September was highest in September, largely a consequence of a floodplain that developed near the mouth. Species richness was related directly to cladoceran abundance. Cladocerans were dominated numerically by three species, Ceriodaphnia cornuta, Diaphanosoma excisum, and D. sarsi. Most species were accommodated within four assemblages. Conductivity, water velocity, pH and temperature were important to species distribution, particularly velocity and conductivity. The most common assemblage was also the most speciose and occurred in moderate total abundance. The second assemblage was also speciose but low in total abundance. Species abundance in groups 1 and 2 tended to be positively related to conductivity and negatively, but weakly, related to pH and temperature. The third assemblage consisted of a single species and occurred in water of low conductivity while the fourth assemblage contained few species and low in overall abundance.     

Effect of Sulfadiazine on Abundance and Diversity of Denitrifying Bacteria by Determining nirK and nirS Genes in Two Arable Soils

Sulfadiazine (SDZ) is an antibiotic frequently used in agricultural husbandry. Via manuring of excrements of medicated animals, the drug reaches the soil and might impair important biochemical transformation processes performed by microbes, e.g., the nitrogen turnover. We studied the effect of pig manure and SDZ-spiked pig manure on denitrifying bacteria by quantifying nirK and nirS nitrite reductase genes in two arable soils. Addition of manure entailed mainly an increase of nirK-harboring denitrifiers in both soils, whereas in the SDZ-amended treatments, primarily the nirS denitrifiers increased in abundance after the bioavailable SDZ had declined. However, the community composition of nirS nitrite reducers investigated by denaturing gradient gel electrophoresis did not change despite the observed alterations in abundance.     

Effect of Abandonment on Diversity and Abundance of Free-Living Nitrogen-Fixing Bacteria and Total Bacteria in the Cropland Soils of Hulun Buir,Inner Mongolia

In Inner Mongolia, steppe grasslands face desertification or degradation because of human over activity. One of the reasons for this condition is that croplands have been abandoned after inappropriate agricultural management. The soils in these croplands present heterogeneous environments in which conditions affecting microbial growth and diversity fluctuate widely in space and time. In this study, we assessed the molecular ecology of total and free-living nitrogen-fixing bacterial communities in soils from steppe grasslands and croplands that were abandoned for different periods (1, 5, and 25 years) and compared the degree of recovery. The abandoned croplands included in the study were natural restoration areas without human activity. Denaturing gradient gel electrophoresis and quantitative PCR (qPCR) were used to analyze the nifH and 16S rRNA genes to study free-living diazotrophs and the total bacterial community, respectively. The diversities of free-living nitrogen fixers and total bacteria were significantly different between each site (P<0.001). Neither the total bacteria nor nifH gene community structure of a cropland abandoned for 25 years was significantly different from those of steppe grasslands. In contrast, results of qPCR analysis of free-living nitrogen fixers and total bacteria showed significantly high abundance levels in steppe grassland (P<0.01 and P<0.03, respectively). In this study, the microbial communities and their gene abundances were assessed in croplands that had been abandoned for different periods. An understanding of how environmental factors and changes in microbial communities affect abandoned croplands could aid in appropriate soil management to optimize the structures of soil microorganisms.     

水位埋深和微地貌对金川泥炭土壤微生物活性及甲烷功能基因的影响

泥炭沼泽是长期储存碳最有效的陆地生态系统.水文特征和微地貌可能会通过调控微生物群落和功能影响泥炭地碳储存.本研究以长白山金川泥炭沼泽为研究对象,选取-10、-1、0、4、10、13、14和18 cm八个水位埋深,并在各水位埋深点采集臌囊薹草(Carexs chmidtii)草丘和丘间微地貌的土壤样品,以探究水位埋深和微...     

Parasite Prevalence, Abundance, and Diversity in a Semi-free-ranging Colony of Mandrillus sphinx

We examined parasite prevalence, abundance of protozoan cysts and helminth eggs in the feces, and number of parasitic taxa in a population of mandrills (Mandrillus sphinx) in semi-free-ranging conditions in their habitat range, with respect to the annual cycle, sex, age, dominance rank, and female reproductive status. We identified 3 taxa of amebic protozoa (Entamoeba coli, E. histolytica/dispar complex, and Endolimax nana), 1 ciliate protozoa (Balantidium coli), and various nematodes. Prevalence ranged from 1 observation in 874 samples for Trichuris and Mammomonogamus (nematodes) to 100% for Entamoeba coli and Endolimax nana. Daily observation, consistency of fecal samples, and periodic veterinary examination indicated that the mandrills were all healthy, suggesting that the presence of intestinal parasites in the provisioned population is well tolerated. Parasite prevalence, abundance in the feces, and number of taxa varied significantly across the annual cycle. Nematode egg prevalence and abundance were lowest during the dry season. We found no sexual difference and no influence of female dominance rank on parasitic infections. Nematode prevalence increased significantly with age in females, but not in males. There was no influence of age on prevalence of other taxa, abundance in the feces, or number of taxa. Abundance of nematode eggs in the feces was higher in pregnant than in lactating or cycling females. However, births are seasonal in the mandrill colony, and pregnant females were present during the months when nematode egg abundance was also higher in males, suggesting that this may be an influence of climatic seasonality in addition to, or instead of, female status.     

Abundance, Diversity, and Dynamics of Viruses on Microorganisms in Activated Sludge Processes

We examined the abundance of viruses on microorganisms in activated sludge and the dynamics of their community structure. Direct counting with epifluorescence microscopy and pulsed-field gel electrophoresis (PFGE) were applied to 20 samples from 14 full-scale wastewater treatment plants (wwtps) treating municipal, industrial, or animal wastewater. Furthermore, to observe the dynamics of viral community structure over time, a laboratory-scale sequencing batch reactor was operated for 58 days. The concentrations of virus particles in the wwtps, as quantified by epifluorescence microscopy, ranged from 4.2 × 10⁷ to 3.0 × 10⁹ mL⁻¹. PFGE, improved by the introduction of a higher concentration of Tris–EDTA buffer in the DNA extraction step, was successfully used to profile DNA viruses in the activated sludge. Most of the samples from different wwtps commonly had bands in the 40–70 kb range. In the monitoring of viral DNA size distribution in the laboratory-scale reactor, some bands were observed stably throughout the experimental period, some emerged during the operation, and others disappeared. Rapid emergence and disappearance of two intense bands within 6 days was observed. Our data suggest that viruses—especially those associated with microorganisms—are abundant and show dynamic behavior in activated sludge.     

Diversity of functional genes for methanotrophs in sediments associated with gas hydrates and hydrocarbon seeps in the Gulf of Mexico

Methanotrophs are ubiquitous in soil, fresh water and the open ocean, but have not been well characterized in deep-sea hydrocarbon seeps and gas hydrates, where methane is unusually abundant. Here we report the presence of new functional genes for the aerobic oxidation of methane by methanotrophs in marine sediments associated with gas hydrates and hydrocarbon seeps in the Gulf of Mexico. Samples were collected from two hydrate locations (GC185 and GC234): one hydrocarbon-seep location at a brine pool (GC233) and one background-marine location about 1.2 miles north of the brine pool (NBP). Community DNA was extracted from each location to establish clone libraries for the pmoA functional gene using a PCR-based cloning approach. Three hundred and ninety clones were screened by sequencing and 46 operational taxonomic units were obtained. Eight operational taxonomic units were present in every sample; one of them was predominant and accounted for 22.8-25.3% of each clone library. Principal-component analysis indicated that samples GC185 and GC234 were closely related and, along with GC233, were significantly different from NBP. These results indicate that methanotrophic communities may be similarly impacted by hydrocarbons at the gas-hydrate and seep sites, and can be distinguished from methanotrophic communities in the normal marine sediment. Furthermore, cluster analysis showed that 84.8% of operational taxonomic units from all samples formed distinct clusters, which could not be grouped with any published pmoA sequences, indicating that a considerable number of novel methanotrophic species may exist in the Gulf of Mexico.     

Diversity, Activity, and Abundance of Sulfate-Reducing Bacteria in Saline and Hypersaline Soda Lakes

Soda lakes are naturally occurring highly alkaline and saline environments. Although the sulfur cycle is one of the most active element cycles in these lakes, little is known about the sulfate-reducing bacteria (SRB). In this study we investigated the diversity, activity, and abundance of SRB in sediment samples and enrichment cultures from a range of (hyper)saline soda lakes of the Kulunda Steppe in southeastern Siberia in Russia. For this purpose, a polyphasic approach was used, including denaturing gradient gel electrophoresis of dsr gene fragments, sulfate reduction rate measurements, serial dilutions, and quantitative real-time PCR (qPCR). Comparative sequence analysis revealed the presence of several novel clusters of SRB, mostly affiliated with members of the order Desulfovibrionales and family Desulfobacteraceae. We detected sulfate reducers and observed substantial sulfate reducing rates (between 12 and 423 μmol/dm³ day⁻¹) for most lakes, even at a salinity of 475 g/liter. Enrichments were obtained at salt saturating conditions (4 M Na⁺), using H₂ or volatile fatty acids as electron donors, and an extremely halophilic SRB, strain ASO3-1, was isolated. Furthermore, a high dsr gene copy number of 10⁸ cells per ml was detected in a hypersaline lake by qPCR. Our results indicate the presence of diverse and active SRB communities in these extreme ecosystems.