Functional Gene Diversity Research Articles

Functional gene diversity and migration timing in reintroduced Chinook salmon

Reintroductions are used to reestablish populations to historical habitats from which they were extirpated. The long-term success of these efforts will depend on genetic diversity and the ability of reintroduced individuals to adapt to ecological change. We examined variation at circadian clock (OtsClock1b and OmyFbxw11) and reproductive timing (Ots515NWFSC)—associated genes in two threatened spring-run Chinook salmon (Oncorhynchus tshawytscha) populations that are undergoing restoration to historical habitats above dams. We also tested for an association between the genes and individual variation in arrival time to the spawning grounds. Our findings indicate that levels of genetic diversity in reintroduced individuals are similar to those found in previously studied spring, summer, fall and winter-run Chinook salmon populations. Captive-rearing programs established following dam construction and the more recent reintroduction efforts thus appear to have maintained diversity at these genes. We observed temporal (between run-years) and spatial (between populations) patterns of genetic differentiation, but little evidence that selection underlies these differences. However, there was a relationship between the circadian-associated gene, OmyFbxw11, and arrival time to the spawning grounds, and in one year of the study, “early” and “late” arrivers to the spawning grounds were more differentiated at the gene than at neutral markers. Taken together, these findings suggest that reintroduced salmon may be capable of an evolutionary response to ecological shifts that alter the adaptive landscape between fitness and arrival timing to the spawning grounds.

Evolution of new functions de novo and from preexisting genes.

How the enormous structural and functional diversity of new genes and proteins was generated (estimated to be 10(10)-10(12) different proteins in all organisms on earth [Choi I-G, Kim S-H. 2006. Evolution of protein structural classes and protein sequence families. Proc Natl Acad Sci 103: 14056-14061] is a central biological question that has a long and rich history. Extensive work during the last 80 years have shown that new genes that play important roles in lineage-specific phenotypes and adaptation can originate through a multitude of different mechanisms, including duplication, lateral gene transfer, gene fusion/fission, and de novo origination. In this review, we focus on two main processes as generators of new functions: evolution of new genes by duplication and divergence of pre-existing genes and de novo gene origination in which a whole protein-coding gene evolves from a noncoding sequence.

Functional gene composition, diversity and redundancy in microbial stream biofilm communities.

We surveyed the functional gene composition and diversity of microbial biofilm communities in 18 New Zealand streams affected by different types of catchment land use, using a comprehensive functional gene array, GeoChip 3.0. A total of 5,371 nutrient cycling and energy metabolism genes within 65 gene families were detected among all samples (342 to 2,666 genes per stream). Carbon cycling genes were most common, followed by nitrogen cycling genes, with smaller proportions of sulphur, phosphorus cycling and energy metabolism genes. Samples from urban and native forest streams had the most similar functional gene composition, while samples from exotic forest and rural streams exhibited the most variation. There were significant differences between nitrogen and sulphur cycling genes detected in native forest and urban samples compared to exotic forest and rural samples, attributed to contrasting proportions of nitrogen fixation, denitrification, and sulphur reduction genes. Most genes were detected only in one or a few samples, with only a small minority occurring in all samples. Nonetheless, 42 of 65 gene families occurred in every sample and overall proportions of gene families were similar among samples from contrasting streams. This suggests the existence of functional gene redundancy among different stream biofilm communities despite contrasting taxonomic composition.

Modular organization of the white spruce (Picea glauca) transcriptome reveals functional organization and evolutionary signatures.

Summary Transcript profiling has shown the molecular bases of several biological processes in plants but few studies have developed an understanding of overall transcriptome variation. We investigated transcriptome structure in white spruce (Picea glauca), aiming to delineate its modular organization and associated functional and evolutionary attributes.Microarray analyses were used to: identify and functionally characterize groups of co‐expressed genes; investigate expressional and functional diversity of vascular tissue preferential genes which were conserved among Picea species, and identify expression networks underlying wood formation.We classified 22 857 genes as variable (79%; 22 coexpression groups) or invariant (21%) by profiling across several vegetative tissues. Modular organization and complex transcriptome restructuring among vascular tissue preferential genes was revealed by their assignment to coexpression groups with partially overlapping profiles and partially distinct functions. Integrated analyses of tissue‐based and temporally variable profiles identified secondary xylem gene networks, showed their remodelling over a growing season and identified PgNAC‐7 (no apical meristerm (NAM), Arabidopsis transcription activation factor (ATAF) and cup‐shaped cotyledon (CUC) transcription factor 007 in Picea glauca) as a major hub gene specific to earlywood formation.Reference profiling identified comprehensive, statistically robust coexpressed groups, revealing that modular organization underpins the evolutionary conservation of the transcriptome structure.

Potential functional gene diversity involved in methanogenesis and methanogenic community structure in Indian buffalo (Bubalus bubalis) rumen.

Understanding the methanogen community structure and methanogenesis from Bubalus bubalis in India may be beneficial to methane mitigation. Our current understanding of the microbial processes leading to methane production is incomplete, and further advancement in the knowledge of methanogenesis pathways would provide means to manipulate its emission in the future. In the present study, we evaluated the methanogenic community structure in the rumen as well as their potential genes involved in methanogenesis. The taxonomic and metabolic profiles of methanogens were assessed by shotgun sequencing of rumen metagenome by Ion Torrent semiconductor sequencing. The buffalo rumen contained representative genera of all the families of methanogens. Members of Methanobacteriaceae were found to be dominant, followed by Methanosarcinaceae, Methanococcaceae, Methanocorpusculaceae, and Thermococcaceae. A total of 60 methanogenic genera were detected in buffalo rumen. Methanogens related to the genera Methanobrevibacter, Methanosarcina, Methanococcus, Methanocorpusculum, Methanothermobacter, and Methanosphaera were predominant, representing >70 % of total archaeal sequences. The metagenomic dataset indicated the presence of genes involved in the methanogenesis and acetogenesis pathways, and the main functional genes were those of key enzymes in the methanogenesis. Sequences related to CoB--CoM heterodisulfide reductase, methyl coenzyme M reductase, f420-dependent methylenetetrahydromethanopterin reductase, and formylmethanofuran dehydrogenase were predominant in rumen. In addition, methenyltetrahydrofolate cyclohydrolase, methylenetetrahydrofolate dehydrogenase, 5,10-methylenetetrahydrofolate reductase, and acetyl-coenzyme A synthetase were also recovered.

Evolutionary Character of Alternative Splicing in Plants.

Alternative splicing (AS) is one of the most important ways to enhance the functional diversity of genes. Huge amounts of data have been produced by microarray, expressed sequence tag, and RNA-seq, and plenty of methods have been developed specifically for this task. The most frequently asked questions in previous research were as follows. What is the content rate of AS genes among the whole gene set? How many AS types are presented in the genome, and which type is dominant? How about the conservation ability of AS among different species? Which kinds of isoforms from some genes have the environmental response to help individual adaptation? Based on this background, we collected analysis results from 17 species to try to map out the landscape of AS studies in plants. We have noted the shortages of previous results, and we appeal to all scientists working in the AS field to make a standard protocol so that analyses between different projects are comparable.

Metagenomic-based study of the phylogenetic and functional gene diversity in Galápagos land and marine iguanas.

In this study, a metagenome-based analysis of the fecal samples from the macrophytic algae-consuming marine iguana (MI; Amblyrhynchus cristatus) and terrestrial biomass-consuming land iguanas (LI; Conolophus spp.) was conducted. Phylogenetic affiliations of the fecal microbiome were more similar between both iguanas than to other mammalian herbivorous hosts. However, functional gene diversities in both MI and LI iguana hosts differed in relation to the diet, where the MI fecal microbiota had a functional diversity that clustered apart from the other terrestrial-biomass consuming reptilian and mammalian hosts. A further examination of the carbohydrate-degrading genes revealed that several of the prevalent glycosyl hydrolases (GH), glycosyl transferases (GT), carbohydrate binding modules (CBM), and carbohydrate esterases (CE) gene classes were conserved among all examined herbivorous hosts, reiterating the important roles these genes play in the breakdown and metabolism of herbivorous diets. Genes encoding some classes of carbohydrate-degrading families, including GH2, GH13, GT2, GT4, CBM50, CBM48, CE4, and CE11, as well as genes associated with sulfur metabolism and dehalogenation, were highly enriched or unique to the MI. In contrast, gene sequences that relate to archaeal methanogenesis were detected only in LI fecal microbiome, and genes coding for GH13, GH66, GT2, GT4, CBM50, CBM13, CE4, and CE8 carbohydrate active enzymes were highly abundant in the LI. Bacterial populations were enriched on various carbohydrates substrates (e.g., glucose, arabinose, xylose). The majority of the enriched bacterial populations belong to genera Clostridium spp. and Enterococcus spp. that likely accounted for the high prevalence of GH13 and GH2, as well as the GT families (e.g., GT2, GT4, GT28, GT35, and GT51) that were ubiquitously present in the fecal microbiota of all herbivorous hosts.

Abundance and diversity of functional genes involved in the degradation of aromatic hydrocarbons in Antarctic soils and sediments around Syowa Station.

Hydrocarbon catabolic genes were investigated in soils and sediments in nine different locations around Syowa Station, Antarctica, using conventional PCR, real-time PCR, cloning, and sequencing analysis. Polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase (PAH-RHD)-coding genes from both Gram-positive and Gram-negative bacteria were observed. Clone libraries of Gram-positive RHD genes were related to (i) nidA3 of Mycobacterium sp. py146, (ii) pdoA of Terrabacter sp. HH4, (iii) nidA of Diaphorobacter sp. KOTLB, and (iv) pdoA2 of Mycobacterium sp. CH-2, with 95-99% similarity. Clone libraries of Gram-negative RHD genes were related to the following: (i) naphthalene dioxygenase of Burkholderia glathei, (ii) phnAc of Burkholderia sartisoli, and (iii) RHD alpha subunit of uncultured bacterium, with 41-46% similarity. Interestingly, the diversity of the Gram-positive RHD genes found around this area was higher than those of the Gram-negative RHD genes. Real-time PCR showed different abundance of dioxygenase genes between locations. Moreover, the PCR-denaturing gradient gel electrophoresis (DGGE) profile demonstrated diverse bacterial populations, according to their location. Forty dominant fragments in the DGGE profiles were excised and sequenced. All of the sequences belonged to ten bacterial phyla: Proteobacteria, Actinobacteria, Verrucomicrobia, Bacteroidetes, Firmicutes, Chloroflexi, Gemmatimonadetes, Cyanobacteria, Chlorobium, and Acidobacteria. In addition, the bacterial genus Sphingomonas, which has been suggested to be one of the major PAH degraders in the environment, was observed in some locations. The results demonstrated that indigenous bacteria have the potential ability to degrade PAHs and provided information to support the conclusion that bioremediation processes can occur in the Antarctic soils and sediments studied here.

Redox potential and microbial functional gene diversity in wetland sediments under simulated warming conditions: implications for phosphorus mobilization

Microbial-driven biogeochemical cycles in wetlands impacted by global warming pose a potential downstream eutrophication risk. However, the consequences of ongoing warming on the functional and metabolic potential of sediment microbial communities are largely unknown. We incubated sediment samples under both ambient temperature conditions (control) and simulated warming conditions of 5°C above ambient temperature (warmed) using a novel field microcosm system. In warmed samples, we observed in situ a decreased thickness of the oxidized sediment layer and associated lower sediment redox potential. GeoChip 4.0, a comprehensive functional gene microarray, demonstrated that many functional genes that are involved in oxidation–reduction reactions and in phosphorus (P) degradation were preferentially enriched under warming conditions. The enriched genes included those genes encoding carbon monoxide dehydrogenase, acetyl-CoA carboxylase biotin carboxylase (ppc), and ribulose-1,5-bisphosphate carboxylase (Rubisco) for carbon fixation; nitrate reductases (narG) and nitrous oxide reductases (nosZ) for denitrification; cytochrome c for metal reduction; and exopolyphosphatase (ppx) for polyphosphate degradation. The redox potential was one of the most significant parameters linked to microbial functional gene structure. These results demonstrate that the enhanced hypoxia and anaerobic metabolic pathways accelerated sediment P mobilization in freshwater wetland subject to warming, raising the potential of water eutrophication.

Metagenomic approach reveals variation of microbes with arsenic and antimony metabolism genes from highly contaminated soil.

Microbes have great potential for arsenic (As) and antimony (Sb) bioremediation in heavily contaminated soil because they have the ability to biotransform As and Sb to species that have less toxicity or are more easily removed. In this study, we integrated a metagenomic method with physicochemical characterization to elucidate the composition of microbial community and functional genes (related to As and Sb) in a high As (range from 34.11 to 821.23 mg kg−1) and Sb (range from 226.67 to 3923.07 mg kg−1) contaminated mine field. Metagenomic analysis revealed that microbes from 18 phyla were present in the 5 samples of soil contaminated with high As and Sb. Moreover, redundancy analysis (RDA) of the relationship between the 18 phyla and the concentration of As and Sb demonstrated that 5 phyla of microbes, i.e. Actinobacteria, Firmicutes, Nitrospirae, Tenericutes and Gemmatimonadetes were positively correlated with As and Sb concentration. The distribution, diversity and abundance of functional genes (including arsC, arrA, aioA, arsB and ACR3) were much higher for the samples containing higher As and Sb concentrations. Based on correlation analysis, the results showed a positive relationship between arsC-like (R2 = 0.871) and aioA-like (R2 = 0.675) gene abundance and As concentration, and indicated that intracellular As(V) reduction and As(III) oxidation could be the dominant As detoxification mechanism enabling the microbes to survive in the environment. This study provides a direct and reliable reference on the diversity of microbial community and functional genes in an extremely high concentration As- and Sb-contaminated environment.

GeoChip-based analysis of microbial community of a combined nitritation-anammox reactor treating anaerobic digestion supernatant

A combined nitritation-anammox reactor was established to treat anaerobic digestion supernatant. The reactor achieved a nitrogen loading rate of 0.5 kg N/(m3·d) and total nitrogen removal efficiency of 85% after 140 days' operation. To examine the microbial community responsible for the process, GeoChip 4.0, a high-throughput, microarray-based metagenomic tool, was adopted to measure microbial functional potential under different percentages of digestion supernatant. Intriguingly, our results showed that microbial community composition in a stably functioning bioreactor were significantly different under varying environmental conditions. Functional gene diversities decreased with increasing percentages of digestion supernatant. Genes involved in organic remediation and metal resistance were highly abundant, revealing new metabolic potentials in addition to nitrogen and carbon removal. Compared to the significant decrease of genes involved in denitrification and nitrification caused by inhibition of the digestion supernatant, relative abundances of genes for anammox remained relatively stable. This could be partially attributed to the protection of biofilm, which was vital for the stable performance of nitrogen removal. In addition, nitrogen compounds, C/N ratio and the operation parameters (pH and temperature) were the key variables shaping the microbial community, contributing to a total of 76.64% of the variance of the reactor.

Functional gene arrays-based analysis of fecal microbiomes in patients with liver cirrhosis.

BackgroundHuman gut microbiota plays an important role in the pathogenesis of cirrhosis complications. Although the phylogenetic diversity of intestinal microbiota in patients with liver cirrhosis has been examined in several studies, little is known about their functional composition and structure.ResultsTo characterize the functional gene diversity of the gut microbiome in cirrhotic patients, we recruited a total of 42 individuals, 12 alcoholic cirrhosis patients, 18 hepatitis B virus (HBV)-related cirrhosis patients, and 12 normal controls. We determined the functional structure of these samples using a specific functional gene array, which is a combination of GeoChip for monitoring biogeochemical processes and HuMiChip specifically designed for analyzing human microbiomes. Our experimental data showed that the microbial community functional composition and structure were dramatically distinctive in the alcoholic cirrhosis. Various microbial functional genes involved in organic remediation, stress response, antibiotic resistance, metal resistance, and virulence were highly enriched in the alcoholic cirrhosis group compared to the control group and HBV-related cirrhosis group. Cirrhosis may have distinct influences on metabolic potential of fecal microbial communities. The abundance of functional genes relevant to nutrient metabolism, including amino acid metabolism, lipid metabolism, nucleotide metabolism, and isoprenoid biosynthesis, were significantly decreased in both alcoholic cirrhosis group and HBV-related cirrhosis group. Significant correlations were observed between functional gene abundances and Child-Pugh scores, such as those encoding aspartate-ammonia ligase, transaldolase, adenylosuccinate synthetase and IMP dehydrogenase.ConclusionsFunctional gene array was utilized to study the gut microbiome in alcoholic and HBV-related cirrhosis patients and controls in this study. Our array data indicated that the functional composition of fecal microbiomes was heavily influenced by cirrhosis, especially by alcoholic cirrhosis. This study provides new insights into the functional potentials and activity of gut microbiota in cirrhotic patients with different etiologies.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-753) contains supplementary material, which is available to authorized users.

Microbial redox processes in deep subsurface environments and the potential application of (per)chlorate in oil reservoirs.

The ability of microorganisms to thrive under oxygen-free conditions in subsurface environments relies on the enzymatic reduction of oxidized elements, such as sulfate, ferric iron, or CO2, coupled to the oxidation of inorganic or organic compounds. A broad phylogenetic and functional diversity of microorganisms from subsurface environments has been described using isolation-based and advanced molecular ecological techniques. The physiological groups reviewed here comprise iron-, manganese-, and nitrate-reducing microorganisms. In the context of recent findings also the potential of chlorate and perchlorate [jointly termed (per)chlorate] reduction in oil reservoirs will be discussed. Special attention is given to elevated temperatures that are predominant in the deep subsurface. Microbial reduction of (per)chlorate is a thermodynamically favorable redox process, also at high temperature. However, knowledge about (per)chlorate reduction at elevated temperatures is still scarce and restricted to members of the Firmicutes and the archaeon Archaeoglobus fulgidus. By analyzing the diversity and phylogenetic distribution of functional genes in (meta)genome databases and combining this knowledge with extrapolations to earlier-made physiological observations we speculate on the potential of (per)chlorate reduction in the subsurface and more precisely oil fields. In addition, the application of (per)chlorate for bioremediation, souring control, and microbial enhanced oil recovery are addressed.

Soil microbial gene diversity in natural broadleaf forests on Gaoligongshan Mountain

Soil microorganisms are among the most important ecosystem components, and they play key roles in biogeochemical cycling, such as carbon and nitrogen cycling. Because of limits in methodology, our understanding of the detailed biological processes in soil microbial communities and their functional activity remains limited. In this study, soil microbial functional gene diversity in broadleaf forests on Gaoligongshan Mountain, Yunnan Province, China, was analyzed by Geochip 2.0, a microbial functional gene array. The array contained 24243 oligonucleotide probes from over 150 functional gene families that targeted key functional genes involved in various ecological and environmental processes, such as carbon and nitrogen cycling. Thus, it provided rapid, specific, sensitive, and potentially quantitative data on microbial communities and was useful for studying the functional diversity and dynamics of microbial communities in different natural environments. A total of 2273 microbial functional genes involved in carbon degradation, carbon fixation, methane oxidation and production, nitrogen cycling, phosphorus utilization, sulphur cycling, organic remediation, metal resistance, energy process, and other categories were detected in five soil samples, and their Shannon-Weaver indexes ranged from 5.39 to 6.91. The soil microbial diversity and abundance in evergreen broadleaf forest was higher than in coniferous and deciduous broadleaf forests. Fifteen and twelve gene categories involved in carbon and nitrogen cycling were observed, respectively. The diversity and abundance of genes involved in carbon and nitrogen cycling differed among the sampling sites. These results showed that different microbial processes involved in element cycling existed in these soil-sampling sites. Canonical correspondence analysis showed that soil organic carbon, soil moisture, soil temperature, and plant diversity may be the key environmental variables shaping the microbial community structure. Variation partitioning analysis showed that soil moisture, soil temperature, and plant Shannon-Weaver index can explain 25.79%, 25.83%, and 18.94% of the community composition, respectively.

Polymorphism among RFL-PPR homologs in sunflower (Helianthus annuus L.) lines with varying ability for the suppression of the cytoplasmic male sterility phenotype

A complex comparative genetic approach was used for the investigation of the structural and functional diversity of genes for the restoration of sunflower pollen fertility. It includes (i) hybridological analysis; (ii) analysis of polymorphism among EST fragments.homologous to the known Rf genes that contain repeated motives of 35 amino acids (RFL-PPR); (iii) the development of molecular markers. Monogenic segregation in three interline cross combinations and the results of molecular marker analysis confirmed the allelic differences of parental lines in the Mendelian locus for CMS PET1 pollen fertility restoration. Introns were found in two RFL-PPR fragments. Two allelic variants of the QHL12D20 fragment were detected among the sixty lines of the sunflower genetic collection. An intron of QHL12D20 fragment was homologous to an intron of the AHBP-1B gene; the product of this gene-has a similarity with the transcription factor of the bZIP-family of Arabidopsis. A relationship between the QHL12D20 polymorphism and the functional state of the Rfl locus was revealed.

The functional diversity of essential genes required for mammalian cardiac development.

Genes required for an organism to develop to maturity (for which no other gene can compensate) are considered essential. The continuing functional annotation of the mouse genome has enabled the identification of many essential genes required for specific developmental processes including cardiac development. Patterns are now emerging regarding the functional nature of genes required at specific points throughout gestation. Essential genes required for development beyond cardiac progenitor cell migration and induction include a small and functionally homogenous group encoding transcription factors, ligands and receptors. Actions of core cardiogenic transcription factors from the Gata, Nkx, Mef, Hand, and Tbx families trigger a marked expansion in the functional diversity of essential genes from midgestation onwards. As the embryo grows in size and complexity, genes required to maintain a functional heartbeat and to provide muscular strength and regulate blood flow are well represented. These essential genes regulate further specialization and polarization of cell types along with proliferative, migratory, adhesive, contractile, and structural processes. The identification of patterns regarding the functional nature of essential genes across numerous developmental systems may aid prediction of further essential genes and those important to development and/or progression of disease. genesis 52:713–737, 2014.

Detecting nitrous oxide reductase (NosZ) genes in soil metagenomes: method development and implications for the nitrogen cycle.

ABSTRACTMicrobial activities in soils, such as (incomplete) denitrification, represent major sources of nitrous oxide (N2O), a potent greenhouse gas. The key enzyme for mitigating N2O emissions is NosZ, which catalyzes N2O reduction to N2. We recently described “atypical” functional NosZ proteins encoded by both denitrifiers and nondenitrifiers, which were missed in previous environmental surveys (R. A. Sanford et al., Proc. Natl. Acad. Sci. U. S. A. 109:19709–19714, 2012, doi:10.1073/pnas.1211238109). Here, we analyzed the abundance and diversity of both nosZ types in whole-genome shotgun metagenomes from sandy and silty loam agricultural soils that typify the U.S. Midwest corn belt. First, different search algorithms and parameters for detecting nosZ metagenomic reads were evaluated based on in silico-generated (mock) metagenomes. Using the derived cutoffs, 71 distinct alleles (95% amino acid identity level) encoding typical or atypical NosZ proteins were detected in both soil types. Remarkably, more than 70% of the total nosZ reads in both soils were classified as atypical, emphasizing that prior surveys underestimated nosZ abundance. Approximately 15% of the total nosZ reads were taxonomically related to Anaeromyxobacter, which was the most abundant genus encoding atypical NosZ-type proteins in both soil types. Further analyses revealed that atypical nosZ genes outnumbered typical nosZ genes in most publicly available soil metagenomes, underscoring their potential role in mediating N2O consumption in soils. Therefore, this study provides a bioinformatics strategy to reliably detect target genes in complex short-read metagenomes and suggests that the analysis of both typical and atypical nosZ sequences is required to understand and predict N2O flux in soils.

Land use change alters functional gene diversity, composition and abundance in Amazon forest soil microbial communities

Land use change in the Amazon rainforest alters the taxonomic structure of soil microbial communities, but whether it alters their functional gene composition is unknown. We used the highly parallel microarray technology GeoChip 4.0, which contains 83,992 probes specific for genes linked nutrient cycling and other processes, to evaluate how the diversity, abundance and similarity of the targeted genes responded to forest-to-pasture conversion. We also evaluated whether these parameters were reestablished with secondary forest growth. A spatially nested scheme was employed to sample a primary forest, two pastures (6 and 38 years old) and a secondary forest. Both pastures had significantly lower microbial functional genes richness and diversity when compared to the primary forest. Gene composition and turnover were also significantly modified with land use change. Edaphic traits associated with soil acidity, iron availability, soil texture and organic matter concentration were correlated with these gene changes. Although primary and secondary forests showed similar functional gene richness and diversity, there were differences in gene composition and turnover, suggesting that community recovery was not complete in the secondary forest. Gene association analysis revealed that response to ecosystem conversion varied significantly across functional gene groups, with genes linked to carbon and nitrogen cycling mostly altered. This study indicates that diversity and abundance of numerous environmentally important genes respond to forest-to-pasture conversion and hence have the potential to affect the related processes at an ecosystem scale.

Indigenous oil-degrading bacteria in crude oil-contaminated seawater of the Yellow sea, China.

Indigenous oil-degrading bacteria play an important role in efficient remediation of polluted marine environments. In this study, we investigated the diversity and abundance of indigenous oil-degrading bacteria and functional genes in crude oil-contaminated seawater of the Dalian coast. The gene copy number bacterial 16S rRNA in total were determined to be about 10(10) copies L(-1) in contaminated seawater and 10(9) copies L(-1) in uncontaminated seawater. Bacteria of Alcanivorax, Marinobacter, Novosphingobium, Rhodococcus, and Pseudoalteromonas were found to be predominant oil-degrading bacteria in the polluted seawater in situ. In addition, bacteria belonging to Algoriphagus, Aestuariibacter, Celeribacter, Fabibacter, Zobellia, Tenacibaculum, Citreicella, Roseivirga, Winogradskyella, Thioclava, Polaribacter, and Pelagibaca were confirmed to be the first time as an oil-degrading bacterium. The indigenous functional enzymes, including AlkB or polycyclic aromatic hydrocarbons ring-hydroxylating dioxygenases α (PAH-RHDα) coding genes from Gram-positive (GP) and Gram-negative bacteria (GN), were revealed and quite diverse. About 10(10) to 10(11) copies L(-1) for the expression of alkB genes were recovered and showed that the two-thirds of all the AlkB sequences were closely related to widely distributed Alcanivorax and Marinobacter isolates. About 10(9) copies L(-1) seawater for the expression of RHDαGN genes in contaminated seawater and showed that almost all RHDαGN sequences were closely related to an uncultured bacterium; however, RHDαGP genes represented only about 10(5) copies L(-1) seawater for the expression of genes in contaminated seawater, and the naphthalene dioxygenase sequences from Rhodococcus and Mycobacterium species were most abundant. Together, their data provide evidence that there exists an active aerobic microbial community indigenous to the coastal area of the Yellow sea that is capable of degrading petroleum hydrocarbons.

Overall functional gene diversity of microbial communities in three full-scale activated sludge bioreactors.

Understanding microbial community composition is thought to be crucial for improving process functioning and stabilities of full-scale activated sludge reactors in wastewater treatment plants (WWTPs). However, functional gene compositions of microbial communities within them have not been clearly elucidated. To gain a complete picture of microbial community, in this study, GeoChip 4.2 was used to profile the overall functional genes of three full-scale activated sludge bioreactors, the 16S rRNA gene diversities of which had been unveiled by 454-pyrosequencing in our previous investigation. Triplicate activated sludge samples from each system were analyzed, with the detection of 38,507 to 40,654 functional genes. A high similarity of 77.3-81.2% shared functional genes was noted among the nine samples, verified by the high 16S rRNA gene similarity with shared operational taxonomic units (OTUs) constituting 66.4-70.0% of the detected sequences in each system. Correlation analyses showed that the abundances of a wide array of functional genes were associated with system performances. For example, the abundances of carbon degradation genes were strongly correlated to chemical oxygen demand (COD) removal efficiencies (r = 0.8697, P < 0.01). Lastly, we found that sludge retention time (SRT), influent total nitrogen concentrations (TN inf), and dissolved oxygen (DO) concentrations were key environmental factors shaping the overall functional genes. Together, the results revealed vast functional gene diversity and some links between the functional gene compositions and microbe-mediated processes.