The Nutrient Status of Mgazana,a Warm Temperate Mangrove Estuary in the Transkei,Eastern Cape,South Africa

Mgazana, a rural southern African mangrove system, was visited monthly from August, 1995 to February, 1997 to collect water samples for nutrient analysis. Surface and bottom samples were taken during spring low tide at seven stations along the estuary and the following physico-chemical parameters measured: river flow, temperature, salinity, oxygen, transparency, ammonia, nitrite, nitrate, phosphate, inorganic carbon (IC), organic carbon (OC), total carbon (TC), soluble nitrogen (SN), particulate nitrogen (PN) and total nitrogen (TN). Using correlation matrix analysis and ANOVA, river flow was found to affect estuarine salinity, transparency and stratification, which influenced nutrient dynamics. Significant seasonal (winter and summer) differences were found for temperature, river flow, nitrate, SN, TN, IC and OC. Most nutrients were significantly correlated with river flow showing gradients down the estuary, indicating allochthonous input from the catchment. OC levels within the estuary were high, probably due to autochthonous mangrove leaf-fall processing by the various in-fauna, but high levels measured at the head of the estuary during high river flow suggested additional allochthonous input from coastal forest litter. Conversely, IC was negatively correlated with river flow suggesting that autochthonous faunal and microbial mineralisation of organic matter occurs within creeks, which is then diluted by increased stream-flow. An N:P ratio of 2.7:1 was obtained for this rural mangrove system, which was low compared with Spartina-based East Cape estuaries subject to urban, industrial and agricultural pollution.     

Analysis of the global ocean sampling (GOS) project for trends in iron uptake by surface ocean microbes

Microbial metagenomes are DNA samples of the most abundant, and therefore most successful organisms at the sampling time and location for a given cell size range. The study of microbial communities via their DNA content has revolutionized our understanding of microbial ecology and evolution. Iron availability is a critical resource that limits microbial communities' growth in many oceanic areas. Here, we built a database of 2319 sequences, corresponding to 140 gene families of iron metabolism with a large phylogenetic spread, to explore the microbial strategies of iron acquisition in the ocean's bacterial community. We estimate iron metabolism strategies from metagenome gene content and investigate whether their prevalence varies with dissolved iron concentrations obtained from a biogeochemical model. We show significant quantitative and qualitative variations in iron metabolism pathways, with a higher proportion of iron metabolism genes in low iron environments. We found a striking difference between coastal and open ocean sites regarding Fe(2+) versus Fe(3+) uptake gene prevalence. We also show that non-specific siderophore uptake increases in low iron open ocean environments, suggesting bacteria may acquire iron from natural siderophore-like organic complexes. Despite the lack of knowledge of iron uptake mechanisms in most marine microorganisms, our approach provides insights into how the iron metabolic pathways of microbial communities may vary with seawater iron concentrations.     

Metagenomic insights into strategies of carbon conservation and unusual sulfur biogeochemistry in a hypersaline Antarctic lake

Organic Lake is a shallow, marine-derived hypersaline lake in the Vestfold Hills, Antarctica that has the highest reported concentration of dimethylsulfide (DMS) in a natural body of water. To determine the composition and functional potential of the microbial community and learn about the unusual sulfur chemistry in Organic Lake, shotgun metagenomics was performed on size-fractionated samples collected along a depth profile. Eucaryal phytoflagellates were the main photosynthetic organisms. Bacteria were dominated by the globally distributed heterotrophic taxa Marinobacter, Roseovarius and Psychroflexus. The dominance of heterotrophic degradation, coupled with low fixation potential, indicates possible net carbon loss. However, abundant marker genes for aerobic anoxygenic phototrophy, sulfur oxidation, rhodopsins and CO oxidation were also linked to the dominant heterotrophic bacteria, and indicate the use of photo- and lithoheterotrophy as mechanisms for conserving organic carbon. Similarly, a high genetic potential for the recycling of nitrogen compounds likely functions to retain fixed nitrogen in the lake. Dimethylsulfoniopropionate (DMSP) lyase genes were abundant, indicating that DMSP is a significant carbon and energy source. Unlike marine environments, DMSP demethylases were less abundant, indicating that DMSP cleavage is the likely source of high DMS concentration. DMSP cleavage, carbon mixotrophy (photoheterotrophy and lithoheterotrophy) and nitrogen remineralization by dominant Organic Lake bacteria are potentially important adaptations to nutrient constraints. In particular, carbon mixotrophy relieves the extent of carbon oxidation for energy production, allowing more carbon to be used for biosynthetic processes. The study sheds light on how the microbial community has adapted to this unique Antarctic lake environment.     

Microbial extracellular electron transfer and its relevance to iron corrosion

Extracellular electron transfer (EET) is a microbial metabolism that enables efficient electron transfer between microbial cells and extracellular solid materials. Microorganisms harbouring EET abilities have received considerable attention for their various biotechnological applications, including bioleaching and bioelectrochemical systems. On the other hand, recent research revealed that microbial EET potentially induces corrosion of iron structures. It has been well known that corrosion of iron occurring under anoxic conditions is mostly caused by microbial activities, which is termed as microbiologically influenced corrosion (MIC). Among diverse MIC mechanisms, microbial EET activity that enhances corrosion via direct uptake of electrons from metallic iron, specifically termed as electrical MIC (EMIC), has been regarded as one of the major causative factors. The EMIC‐inducing microorganisms initially identified were certain sulfate‐reducing bacteria and methanogenic archaea isolated from marine environments. Subsequently, abilities to induce EMIC were also demonstrated in diverse anaerobic microorganisms in freshwater environments and oil fields, including acetogenic bacteria and nitrate‐reducing bacteria. Abilities of EET and EMIC are now regarded as microbial traits more widespread among diverse microbial clades than was thought previously. In this review, basic understandings of microbial EET and recent progresses in the EMIC research are introduced.     

Metagenomic analysis of stress genes in microbial mat communities from Antarctica and the High Arctic

Polar and alpine microbial communities experience a variety of environmental stresses, including perennial cold and freezing; however, knowledge of genomic responses to such conditions is still rudimentary. We analyzed the metagenomes of cyanobacterial mats from Arctic and Antarctic ice shelves, using high-throughput pyrosequencing to test the hypotheses that consortia from these extreme polar habitats were similar in terms of major phyla and subphyla and consequently in their potential responses to environmental stresses. Statistical comparisons of the protein-coding genes showed similarities between the mats from the two poles, with the majority of genes derived from Proteobacteria and Cyanobacteria; however, the relative proportions differed, with cyanobacterial genes more prevalent in the Antarctic mat metagenome. Other differences included a higher representation of Actinobacteria and Alphaproteobacteria in the Arctic metagenomes, which may reflect the greater access to diasporas from both adjacent ice-free lands and the open ocean. Genes coding for functional responses to environmental stress (exopolysaccharides, cold shock proteins, and membrane modifications) were found in all of the metagenomes. However, in keeping with the greater exposure of the Arctic to long-range pollutants, sequences assigned to copper homeostasis genes were statistically (30%) more abundant in the Arctic samples. In contrast, more reads matching the sigma B genes were identified in the Antarctic mat, likely reflecting the more severe osmotic stress during freeze-up of the Antarctic ponds. This study underscores the presence of diverse mechanisms of adaptation to cold and other stresses in polar mats, consistent with the proportional representation of major bacterial groups.     

Abundance and distribution of bacterioplankton in the Gambia River,West Africa

Four ecological zones of the Gambia River were sampled during four different hydrologic seasons for determination of microbial, nutrient, and physical parameters. A Greco-Latin Square experimental design was used to define the particular transect, station, depth, and tide/time-of-day of samples taken. Ranges of total bacterioplankton densities (10⁶ cells/ml) were similar to those of tropical and temperate environments. Numbers of free bacteria were similar temporally, whereas attached bacteria numbers were greater during periods of high stream flows when suspended solids concentrations were higher. Free bacteria were usually twice as numerous in the freshwater zones than in the estuarine zones. Attached bacterial densities were approximately four times greater in the estuarine zones than in the freshwater zones. Uptake of³H-glucose on both a sample volume and per-cell basis increased from the early stages of the flood (6.95±SE 1.37 ng/liter/hour and 3.8 pg/hour/10⁶ cells, respectively) and reached observed annual maximums during the dry season (21.01±SE 3.05 ng/ liter/hour and 13.0 pg/hour/10⁶ cells, respectively). Spatially,³H-glucose uptake per sample volume and per cell was highest in the upper river zone and lowest in the lower estuary zone. The lower estuary zone consistently acted out of concert with the other river zones in terms of³H-glucose and¹⁴C-bicarbonate uptake. Analysis of variance (ANOVA) indicated that free and attached bacterioplankton densities were not homogeneous among transects, stations, depths, and tide/time-of-day at the different zones during the four hydrologic seasons. The results suggested that heterotrophy overshadowed autotrophy in the river and that the bacterial abundance, distribution, and glucose uptake activity in this tropical floodplain river were greatly influenced by the annual flood and the presence of extensive mangrove forests in the estuary.     

Seasonal changes in bacterial and archaeal gene expression patterns across salinity gradients in the Columbia River coastal margin

Through their metabolic activities, microbial populations mediate the impact of high gradient regions on ecological function and productivity of the highly dynamic Columbia River coastal margin (CRCM). A 2226-probe oligonucleotide DNA microarray was developed to investigate expression patterns for microbial genes involved in nitrogen and carbon metabolism in the CRCM. Initial experiments with the environmental microarrays were directed toward validation of the platform and yielded high reproducibility in multiple tests. Bioinformatic and experimental validation also indicated that >85% of the microarray probes were specific for their corresponding target genes and for a few homologs within the same microbial family. The validated probe set was used to query gene expression responses by microbial assemblages to environmental variability. Sixty-four samples from the river, estuary, plume, and adjacent ocean were collected in different seasons and analyzed to correlate the measured variability in chemical, physical and biological water parameters to differences in global gene expression profiles. The method produced robust seasonal profiles corresponding to pre-freshet spring (April) and late summer (August). Overall relative gene expression was high in both seasons and was consistent with high microbial abundance measured by total RNA, heterotrophic bacterial production, and chlorophyll a. Both seasonal patterns involved large numbers of genes that were highly expressed relative to background, yet each produced very different gene expression profiles. April patterns revealed high differential gene expression in the coastal margin samples (estuary, plume and adjacent ocean) relative to freshwater, while little differential gene expression was observed along the river-to-ocean transition in August. Microbial gene expression profiles appeared to relate, in part, to seasonal differences in nutrient availability and potential resource competition. Furthermore, our results suggest that highly-active particle-attached microbiota in the Columbia River water column may perform dissimilatory nitrate reduction (both dentrification and DNRA) within anoxic particle microniches.     

Metagenomic analyses of drinking water receiving different disinfection treatments

A metagenome-based approach was used to assess the taxonomic affiliation and function potential of microbial populations in free-chlorine-treated (CHL) and monochloramine-treated (CHM) drinking water (DW). In all, 362,640 (averaging 544 bp) and 155,593 (averaging 554 bp) pyrosequencing reads were analyzed for the CHL and CHM samples, respectively. Most annotated proteins were found to be of bacterial origin, although eukaryotic, archaeal, and viral proteins were also identified. Differences in community structure and function were noted. Most notably, Legionella-like genes were more abundant in the CHL samples while mycobacterial genes were more abundant in CHM samples. Genes associated with multiple disinfectant mechanisms were identified in both communities. Moreover, sequences linked to virulence factors, such as antibiotic resistance mechanisms, were observed in both microbial communities. This study provides new insights into the genetic network and potential biological processes associated with the molecular microbial ecology of DW microbial communities.     

Riverine macrophytes control seasonal nutrient uptake via both physical and biological pathways

1. In low-gradient, macrophyte-rich rivers, we expect that the significant change in macrophyte biomass among seasons will strongly influence both biological activity and hydraulic conditions resulting in significant effects on nutrient dynamics. Understanding seasonal variation will improve modelling of nutrient transport in river networks, including annual estimations of export, which could optimise decision-making and management outcomes.
2. We explored the relationships among seasonal differences in reach-scale nutrient uptake, macrophyte abundance, solute transport and transient storage in the River Gudenå (Denmark), a large macrophyte-rich river. We used the minimal pulse addition technique to measure uptake of ammonium, nitrate, soluble reactive phosphorus, as well as reach-scale metabolism, and surface transient storage in spring, summer, and autumn.
3. We found that riverine uptake changed among seasons and was linked to macrophyte biomass via both biological activity, reflected in reach-scale metabolism, and through physical processes, as solute transport was influenced by longitudinal dispersion. In this macrophyte-rich river, seasonal changes in macrophyte biomass affected contact time between the water and biota, which influenced ammonium and soluble reactive phosphorus uptake. Using stoichiometric scaling of reach-scale metabolism, we found that seasonal variation also influenced the relative contributions of autotrophic and heterotrophic biota in assimilatory uptake.
4. In summary, riverine nutrient uptake was not static, highlighting the importance of seasonality, with significant implications for modelling of nutrient export in river networks. Moreover, current management strategies that remove macrophyte biomass (i.e. weed cutting and dredging) will short-circuit the positive effects of enhanced nutrient uptake resulting from abundant macrophytes in rivers.

     

Bacterial diversity of water and sediment in the Changjiang estuary and coastal area of the East China Sea

The Changjiang estuary and the coastal area of the East China Sea (ECS) represent important interfaces of terrestrial and marine environments. This study included analyses of water and sediments collected during different seasons in these regions to determine the composition of microbial assemblages by means of 16S rRNA gene clone libraries. We retrieved 1946 sequences and 779 distinct operational taxonomic units from 36 clone libraries. Shannon–Weaver diversity index values and rarefaction analysis indicated that bacterial diversity in the sediment samples was much higher than in the water samples. Proteobacteria (72.9%) was the most abundant phylum, followed by Firmicutes (6.4%), Bacteroidetes (4.6%) and Actinobacteria (4.1%). In the water, clone sequences related to Alphaproteobacteria were the most abundant, whereas in the sediment samples, sequences affiliated with Gammaproteobacteria were predominant. Principal coordinate analysis showed that water samples collected from the Changjiang estuary and the ECS clustered separately. However, this spatial pattern could not be observed in sediment samples, which were mainly distinguished from one another by the season. Bacterial diversity in the Changjiang estuary was higher than that in the ECS, which may be the result of the mixing of bacterial communities from the Changjiang River, the estuary and the coastal ocean.     

Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics

Stratified sulfurous lakes are appropriate environments for studying the links between composition and functionality in microbial communities and are potentially modern analogs of anoxic conditions prevailing in the ancient ocean. We explored these aspects in the Lake Banyoles karstic area (NE Spain) through metagenomics and in silico reconstruction of carbon, nitrogen and sulfur metabolic pathways that were tightly coupled through a few bacterial groups. The potential for nitrogen fixation and denitrification was detected in both autotrophs and heterotrophs, with a major role for nitrogen and carbon fixations in Chlorobiaceae. Campylobacterales accounted for a large percentage of denitrification genes, while Gallionellales were putatively involved in denitrification, iron oxidation and carbon fixation and may have a major role in the biogeochemistry of the iron cycle. Bacteroidales were also abundant and showed potential for dissimilatory nitrate reduction to ammonium. The very low abundance of genes for nitrification, the minor presence of anammox genes, the high potential for nitrogen fixation and mineralization and the potential for chemotrophic CO₂ fixation and CO oxidation all provide potential clues on the anoxic zones functioning. We observed higher gene abundance of ammonia-oxidizing bacteria than ammonia-oxidizing archaea that may have a geochemical and evolutionary link related to the dominance of Fe in these environments. Overall, these results offer a more detailed perspective on the microbial ecology of anoxic environments and may help to develop new geochemical proxies to infer biology and chemistry interactions in ancient ecosystems.     

黄河三角洲原生演替中土壤微生物群落结构分析

[目的] 黄河三角洲区域具有重要的湿地生态系统。碱蓬、野大豆和芦苇是该地区典型的盐生植物。本研究针对碱蓬、野大豆和芦苇混生植物的根际土壤微生物群落组成和功能基因进行了分析比较。[方法] 对碱蓬,野大豆-芦苇混生植物的根际微生物菌群和光滩土壤菌群进行了宏基因组测序,使用COG和KEGG数据库对微生物菌群的功能进行了注释和比较。[结果] 本研究结果表明,变形菌门是3个取样点的主要菌门,其在碱蓬、野大豆-芦苇根际土壤中的相对含量比光滩土壤分别多28.8%和10.6%。此外,拟杆菌门、放线菌门和芽单胞菌门是3个取样点中的优势物种。中华根瘤菌属是野大豆-芦苇混生植物根际土壤的最主要的属。对功能基因进行分析表明,光滩土壤中的功能基因的数量多于碱蓬根际土壤和野大豆-芦苇混生植物根际土壤的功能基因数。在这3个位点中,氨基酸代谢、碳水化合物代谢和能量代谢,以及无机离子转运和代谢的基因最多。[结论] 本研究为发掘有价值的微生物资源和海岸带盐碱土壤修复提供了一定的理论基础。     

Comparative metagenomics reveals insights into the deep-sea adaptation mechanism of the microorganisms in Iheya hydrothermal fields

In this study, comparative metagenomic analysis was performed to investigate the genetic profiles of the microbial communities inhabiting the sediments surrounding Iheya North and Iheya Ridge hydrothermal fields. Four samples were used, which differed in their distances from hydrothermal vents. The results showed that genes involved in cell surface structure synthesis, polyamine metabolism and homeostasis, osmoadaptation, pH and Na⁺ homeostasis, and heavy-metal transport were abundant. Pathways for putrescine and spermidine synthesis and transport were identified in the four metagenomes, which possibly participate in the regulation of cytoplasmic pH. Genes involved in the transport of K⁺ and the biosynthesis of glycine betaine, proline, and trehalose, together with genes encoding mechanosensitive channel of small conductance, were contributors of osmoadaptation. Detection of genes encoding F₁F_o-ATPase and cation/proton antiporters indicated critical roles played by pH and sodium homeostasis. Cu²⁺-exporting and Cd²⁺/Zn²⁺-exporting ATPases functioned in the expulsion of toxic metals across cellular membranes. It is noteworthy that the distribution of some genes, such as that encoding cardiolipin synthase, was apparently affected by distance to the vent site. These findings provide insight into microbial adaptation mechanisms in deep-sea sediment environments.     

Phylogenetic diversity and environment-specific distributions of glycosyl hydrolase family 10 xylanases in geographically distant soils

Background

Xylan is one of the most abundant biopolymers on Earth. Its degradation is mediated primarily by microbial xylanase in nature. To explore the diversity and distribution patterns of xylanase genes in soils, samples of five soil types with different physicochemical characters were analyzed.

Methodology/Principal Findings

Partial xylanase genes of glycoside hydrolase (GH) family 10 were recovered following direct DNA extraction from soil, PCR amplification and cloning. Combined with our previous study, a total of 1084 gene fragments were obtained, representing 366 OTUs. More than half of the OTUs were novel (identities of <65% with known xylanases) and had no close relatives based on phylogenetic analyses. Xylanase genes from all the soil environments were mainly distributed in Bacteroidetes, Proteobacteria, Acidobacteria, Firmicutes, Actinobacteria, Dictyoglomi and some fungi. Although identical sequences were found in several sites, habitat-specific patterns appeared to be important, and geochemical factors such as pH and oxygen content significantly influenced the compositions of xylan-degrading microbial communities.

Conclusion/Significance

These results provide insight into the GH 10 xylanases in various soil environments and reveal that xylan-degrading microbial communities are environment specific with diverse and abundant populations.     

Limited gene flow in Uca minax (LeConte 1855) along a tidally influenced river system

For crab larvae, swimming behaviors coupled with the movement of tides suggests that larvae can normally move upstream within estuaries by avoiding ebb tides and actively swimming during flood tides (i.e., flood-tide transport [FTT]). Recently, a 1-D transport model incorporating larval behavior predicted that opposing forces of river discharge and tidal amplitude in the Pee Dee River/Winyah Bay system of South Carolina, USA, could limit dispersal within a single estuary for downstream transport as well as become a dispersal barrier to recruitment of late stage larvae to the freshwater adult habitats of Uca minax (LeConte 1855). We sequenced 394-bp of the mitochondrial cytochrome apoenzyme b for 226 adult U. minax, from four locales along a 49-km stretch of the Pee Dee River/Winyah Bay estuary, above and below the boundary of salt intrusion. Results of an analysis of molecular variance (AMOVA) and an exact test of population differentiation showed a small, but statistically significant (α=0.05) population subdivision among adults of the 4 subpopulations, as well as all subpopulations being significantly differentiated (α=0.05). This pattern fitted with model predictions, which implies that larval transport within the tidally influenced river system is limited.     

Rapid Detection and Quantification of Members of the Archaeal Community by Quantitative PCR Using Fluorogenic Probes

We describe a rapid, reproducible, and sensitive method for detection and quantification of archaea in naturally occurring microbial communities. A domain-specific PCR primer set and a domain-specific fluorogenic probe having strong and weak selectivity, respectively, for archaeal rRNA genes (rDNAs) were designed. A universal PCR primer set and a universal fluorogenic probe for both bacterial and archaeal rDNAs were also designed. Using these primers and probes, we demonstrated that detection and quantification of archaeal rDNAs in controlled microbial rDNA assemblages can be successfully achieved. The system which we designed was also able to detect and quantify archaeal rDNAs in DNA samples obtained not only from environments in which thermophilic archaea are abundant but also from environments in which methanogenic archaea are abundant. Our findings indicate that this method is applicable to culture-independent molecular analysis of microbial communities in various environments.     

Rapid detection and quantification of members of the archaeal community by quantitative PCR using fluorogenic probes

We describe a rapid, reproducible, and sensitive method for detection and quantification of archaea in naturally occurring microbial communities. A domain-specific PCR primer set and a domain-specific fluorogenic probe having strong and weak selectivity, respectively, for archaeal rRNA genes (rDNAs) were designed. A universal PCR primer set and a universal fluorogenic probe for both bacterial and archaeal rDNAs were also designed. Using these primers and probes, we demonstrated that detection and quantification of archaeal rDNAs in controlled microbial rDNA assemblages can be successfully achieved. The system which we designed was also able to detect and quantify archaeal rDNAs in DNA samples obtained not only from environments in which thermophilic archaea are abundant but also from environments in which methanogenic archaea are abundant. Our findings indicate that this method is applicable to culture-independent molecular analysis of microbial communities in various environments.