Robustness of archaeal populations in anaerobic co-digestion of dairy and poultry wastes

The objective of this study is to investigate the responses of methanogen populations to poultry waste addition by comparing the archaeal microbial populations in continuous anaerobic digesters with or without the addition of poultry waste as a co-substrate. Poultry waste was characterized as an organic/nitrogen-rich substrate for anaerobic digestion. Supplementing dilute dairy waste with poultry waste for anaerobic co-digestion to increase organic loading rate by 50% resulted in improved biogas production. Elevated ammonia derived from poultry waste did not lead to process inhibition at the organic loadings tested, demonstrating the feasibility of the anaerobic co-digestion of dairy and poultry wastes for improved treatment efficiency. The stability of the anaerobic co-digestion process was linked to the robust archaeal microbial community, which remained mostly unchanged in community structure following increases in organic loading and ammonia levels. Surprisingly, Crenarchaeota archaeal populations, instead of the Euryarchaeota methanogens, dominated the archaeal communities in the anaerobic digesters. The ecological functions of these abundant non-methanogen archaeal populations in anaerobic digestion remain to be identified.     

Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform

Here we demonstrate a cost effective and scalable microbial ecology sequencing platform using the Ion Torrent Personal Genome Machine (PGM). We assessed both PCR amplified 16S rRNA and shotgun metagenomic approaches and generated 100,000+ to 1,000,000+ reads using 'post-light' based sequencing technology within different sized semi-conductor chips. Further development of Golay barcoded Ion Tags allowed multiplex analyses of microbial communities with substantially reduced costs compared with platforms such as 454/GS-FLX. Using these protocols we assessed the bacterial and archaeal dynamics within covered anaerobic digesters used to treat piggery wastes. Analysis of these sequence data showed that these novel methanogenic waste treatment systems are dominated by bacterial taxa, in particular Clostridium, Synergistia and Bacteroides that were maintained as a stable community over extended time periods. Archaeal community dynamics were more stochastic with the key methanogenic taxa more difficult to resolve, principally due to the poor congruence seen between community structures generated either by nested PCR or metagenomic approaches for archaeal analyses. Our results show that for microbial community structure and function analyses, the PGM platform provides a low cost, scalable and high throughput solution for both Tag sequencing and metagenomic analyses.     

Spatial distribution and abundances of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in mangrove sediments

We investigated the diversity, spatial distribution, and abundances of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in sediment samples of different depths collected from a transect with different distances to mangrove forest in the territories of Hong Kong. Both the archaeal and bacterial amoA genes (encoding ammonia monooxygenase subunit A) from all samples supported distinct phylogenetic groups, indicating the presences of niche-specific AOA and AOB in mangrove sediments. The higher AOB abundances than AOA in mangrove sediments, especially in the vicinity of the mangrove trees, might indicate the more important role of AOB on nitrification. The spatial distribution showed that AOA had higher diversity and abundance in the surface layer sediments near the mangrove trees (0 and 10 m) but lower away from the mangrove trees (1,000 m), and communities of AOA could be clustered into surface and bottom sediment layer groups. In contrast, AOB showed a reverse distributed pattern, and its communities were grouped by the distances between sites and mangrove trees, indicating mangrove trees might have different influences on AOA and AOB community structures. Furthermore, the strong correlations among archaeal and bacterial amoA gene abundances and their ratio with NH₄⁺, salinity, and pH of sediments indicated that these environmental factors have strong influences on AOA and AOB distributions in mangrove sediments. In addition, AOA diversity and abundances were significantly correlated with hzo gene abundances, which encodes the key enzyme for transformation of hydrazine into N₂ in anaerobic ammonium-oxidizing (anammox) bacteria, indicating AOA and anammox bacteria may interact with each other or they are influenced by the same controlling factors, such as NH₄⁺. The results provide a better understanding on using mangrove wetlands as biological treatment systems for removal of nutrients.     

Organic Layer Serves as a Hotspot of Microbial Activity and Abundance in Arctic Tundra Soils

Tundra ecosystem is of importance for its high accumulation of organic carbon and vulnerability to future climate change. Microorganisms play a key role in carbon dynamics of the tundra ecosystem by mineralizing organic carbon. We assessed both ecosystem process rates and community structure of Bacteria, Archaea, and Fungi in different soil layers (surface organic layer and subsurface mineral soil) in an Arctic soil ecosystem located at Spitsbergen, Svalbard during the summer of 2008 by using biochemical and molecular analyses, such as enzymatic assay, terminal restriction fragment length polymorphism (T-RFLP), quantitative polymerase chain reaction (qPCR), and pyrosequencing. Activity of hydrolytic enzymes showed difference according to soil type. For all three microbial communities, the average gene copy number did not significantly differ between soil types. However, archaeal diversities appeared to differ according to soil type, whereas bacterial and fungal diversity indices did not show any variation. Correlation analysis between biogeochemical and microbial parameters exhibited a discriminating pattern according to microbial or soil types. Analysis of the microbial community structure showed that bacterial and archaeal communities have different profiles with unique phylotypes in terms of soil types. Water content and hydrolytic enzymes were found to be related with the structure of bacterial and archaeal communities, whereas soil organic matter (SOM) and total organic carbon (TOC) were related with bacterial communities. The overall results of this study indicate that microbial enzyme activity were generally higher in the organic layer than in mineral soils and that bacterial and archaeal communities differed between the organic layer and mineral soils in the Arctic region. Compared to mineral soil, peat-covered organic layer may represent a hotspot for secondary productivity and nutrient cycling in this ecosystem.     

厌氧铵氧化过程中关键酶及相关分子标记在生态学研究中的应用进展

厌氧铵氧化是由微生物介导的氮素循环过程中的重要途径之一。近20年来,通过对厌氧铵氧化细菌生态学、基因组学和生理代谢特性的探索,人们对其微生物学机制已经有了较多的认识:厌氧铵氧化细菌通过亚硝酸盐还原酶将亚硝酸根离子还原为一氧化氮,进而与铵离子结合在联氨合成酶的作用下生成联氨,最后通过联氨氧化酶的催化产生终产物氮气。同时,对参与这些过程的关键酶及其功能基因的认识有助于选择新的分子标记,从而为研究厌氧铵氧化细菌的多样性和分子生态学特征提供新的工具,以弥补16S rRNA基因特异性相对较低且难以与生态功能关联等方面的不足。对目前已知的参与厌氧铵氧化过程的3种关键酶的研究历程和现状进行了评述,并总结了利用3种功能基因进行厌氧铵氧化细菌生态学研究的最新进展。     

海南东寨港红树林不同植被土壤微生物群落结构比较

【目的】比较不同植被下红树林土壤细菌和古菌的多样性及群落结构,认识红树林土壤微生物资源多样性。【方法】直接提取红树林土壤总DNA,采用细菌通用引物27F/1492R和古菌通用引物Arch21F/Arch958R进行PCR扩增,构建细菌和古菌16S rRNA基因文库,对海南东寨港自然保护区秋茄林、无瓣海桑林和无红树林裸滩土壤的细菌和古菌多样性和群落结构进行分析和比较。【结果】3种土壤样品的细菌类群包括变形细菌门(Proteobacteria)等16个类群,其中变形细菌门(Proteobacteria)与绿屈挠菌门(Chloroflexi)是优势类群;古菌包括6个嗜泉古菌界(Crenarchaeota)类群和7个广域古菌界(Euryarchaeota)类群,分别以Marine Benthic Group C、Marine Benthic Group D为优势类群。多样性指数(H’)和物种丰富度指数(Schao1)表明,本地种秋茄林下土壤细菌和古菌的多样性指数最高,外来种无瓣海桑显著低于秋茄林,甚至明显低于相邻无红树林裸滩沉积物;不同植被下土壤细菌和古菌群落结构存在显著差异,秋茄林土壤微生物群落结构和无红树林裸滩沉积物更相似。【结论】红树林土壤微生物类群丰富,不同植被下土壤细菌和古菌多样性和群落结构存在显著差异。     

Spatial variations in macrobenthic fauna recolonisation in a tropical mangrove bay

Recolonisation by crab species and sediment-infauna taxa (at class level) in artificially regenerated mangrove stands of Avicennia marina, Rhizophora mucronata and Sonneratia alba (5 yr old) were studied using respective bare sites (open without mangroves or denuded) and natural sites (relatively undisturbed) as controls. The controls were chosen based on site history, physical proximity and tidal inundation class in reference to the particular reforested mangrove stand and samples randomly taken. A number of environmental variables were measured; interstitial water salinity and temperature (measured at low tide) were lower, whereas sediment organic matter content was higher in the areas with mangrove cover, with the natural sites having the highest content. The bare sites were generally sandier, whereas the areas with mangrove cover had higher proportions of clay and silt. Generally, there was a higher crab density in the reforested sites than in the bare sites, whereas crab species diversity (Shannon diversity index) did not vary from one site to another for any of the mangrove species. In terms of crab species composition, the reforested sites were more similar (Sørensen similarity coefficient) to the natural sites and less to the bare controls. For sediment-infauna, the reforested sites had a significantly higher density than the respective bare controls, while the natural sites had the highest density. The number of sediment-infauna taxa in both the reforested and natural sites of all the mangrove species was similar and higher than in the comparable bare sites. The results suggest that the reforested sites are supporting more faunal recolonisation, and therefore becoming more akin to the natural mangrove sites in terms of the investigated functional indicators. The findings seem to support the use of artificial mangrove regeneration (in areas where natural regeneration has been impeded by physical conditions or otherwise) as an effective management tool in the restoration and conservation of the functional integrity of degraded mangrove habitats.Key words: Crabs, Environmental variables, Kenya, Recolonisation, Restored mangroves, Sediment-infauna     

Long-term development of tidal mitigation wetlands in Florida

Monitoring periods for compensatory wetland mitigation projects are relatively short, typically 3 to 5 years. Although forested wetlands may require decades to develop structural characteristics similar to those of natural systems, studies that describe long-term trends in site development are rare. Eighteen mitigation sites in Florida that had originally been sampled in 1988 were re-visited in 2005. Changes in mangrove community composition and stand structure occurring over this timeframe at ten of these sites are described and compared with other mangrove wetlands in Florida. Factors limiting development of the remaining sites are discussed. The continued persistence and development of the majority of these mitigation sites indicates that the mitigation process can be successful, at least in terms of compliance with the typical permit requirements. Basal area and height had increased at most sites, and some were difficult to visually distinguish from adjacent natural stands of mangroves. However, even after 13–25 years, stand structure in mangrove mitigation wetlands in Florida still differed from that of natural sites. Although the number of mangrove species was similar, mitigation sites had lower basal area and height than natural sites, and were more dense and complex than natural sites.     

中国红树林生态系统保护空缺分析

红树林作为海岸带重要的生态系统类型,具有维持海岸生物多样性、防风固岸、促淤造陆等重要的生态功能,在气候变化和快速城市化背景下认识红树林受保护状况具有重要意义。以基于遥感解译的红树林分类数据为基础,通过空缺分析,分析了我国红树林的就地保护状况,结果显示我国分布的红树林总面积为264 km~2(尚不含我国港、澳、台的统计数据),其中61.4%在自然保护区内受到保护。从红树林分布的主要省份来看,在海南省分布的红树林面积较少但保护比例高,广西和广东省分布的红树林面积大但受保护面积比例相对较低。在3种红树林类型中,红树-木果楝林和红海榄-木榄林分布面积较小,但受保护的面积都在90%以上,秋茄-桐花树-白骨壤林分布的面积最大,但受保护的面积为52.6%。研究提出自然保护区外红树林分布的关键区域,并建议通过划定生态保护红线等方式来进行保护。     

Biases in community structures of ammonia/ammonium-oxidizing microorganisms caused by insufficient DNA extractions from Baijiang soil revealed by comparative analysis of coastal wetland sediment and rice paddy soil

Repetitive extraction of DNAs from surface sediments of a coastal wetland in Mai Po Nature Reserve (MP) of Hong Kong and surface Baijiang soils from a rice paddy (RP) in Northeast China was conducted to compare the microbial diversity in this study. Community structures of ammonia/ammonium-oxidizing microorganisms in these samples were analyzed by PCR-DGGE technique. The diversity and abundance of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and anaerobic ammonium-oxidizing (anammox) bacteria were also analyzed based on archaeal and bacterial ammonia monooxygenase subunit A encoding (amoA) and anammox bacterial 16S rRNA genes, respectively. DGGE profiles of archaeal and bacterial amoA and anammox bacterial 16S rRNA genes showed a similar pattern among all five repetitively extracted DNA fractions from both MP and RP, except the anammox bacteria in RP, indicating a more diverse anammox community retrieved in the second to the fifth fractions than the first one. Both soil and marine group AOA were detected while soil and coastal group AOB and Scalindua-anammox bacteria were dominant in MP. Soil group AOA and marine group AOB were dominant in RP, while both Scalindua and Kuenenia species were detected in RP. Pearson correlation analysis showed that the abundance of archaeal and bacterial amoA and anammox bacterial 16S rRNA genes was significantly correlated with the DNA concentrations of the five DNA fractions from MP, but not from RP (except the archaeal amoA gene). Results suggest that anammox bacteria diversity may be biased by insufficient DNA extraction of rice paddy soil samples.     

Propionate Oxidation by and Methanol Inhibition of Anaerobic Ammonium-Oxidizing Bacteria

Anaerobic ammonium oxidation (anammox) is a recently discovered microbial pathway and a cost-effective way to remove ammonium from wastewater. Anammox bacteria have been described as obligate chemolithoautotrophs. However, many chemolithoautotrophs (i.e., nitrifiers) can use organic compounds as a supplementary carbon source. In this study, the effect of organic compounds on anammox bacteria was investigated. It was shown that alcohols inhibited anammox bacteria, while organic acids were converted by them. Methanol was the most potent inhibitor, leading to complete and irreversible loss of activity at concentrations as low as 0.5 mM. Of the organic acids acetate and propionate, propionate was consumed at a higher rate (0.8 nmol min⁻¹ mg of protein⁻¹) by Percoll-purified anammox cells. Glucose, formate, and alanine had no effect on the anammox process. It was shown that propionate was oxidized mainly to CO₂, with nitrate and/or nitrite as the electron acceptor. The anammox bacteria carried out propionate oxidation simultaneously with anaerobic ammonium oxidation. In an anammox enrichment culture fed with propionate for 150 days, the relative amounts of anammox cells and denitrifiers did not change significantly over time, indicating that anammox bacteria could compete successfully with heterotrophic denitrifiers for propionate. In conclusion, this study shows that anammox bacteria have a more versatile metabolism than previously assumed.     

Propionate oxidation by and methanol inhibition of anaerobic ammonium-oxidizing bacteria

Anaerobic ammonium oxidation (anammox) is a recently discovered microbial pathway and a cost-effective way to remove ammonium from wastewater. Anammox bacteria have been described as obligate chemolithoautotrophs. However, many chemolithoautotrophs (i.e., nitrifiers) can use organic compounds as a supplementary carbon source. In this study, the effect of organic compounds on anammox bacteria was investigated. It was shown that alcohols inhibited anammox bacteria, while organic acids were converted by them. Methanol was the most potent inhibitor, leading to complete and irreversible loss of activity at concentrations as low as 0.5 mM. Of the organic acids acetate and propionate, propionate was consumed at a higher rate (0.8 nmol min(-1) mg of protein(-1)) by Percoll-purified anammox cells. Glucose, formate, and alanine had no effect on the anammox process. It was shown that propionate was oxidized mainly to CO(2), with nitrate and/or nitrite as the electron acceptor. The anammox bacteria carried out propionate oxidation simultaneously with anaerobic ammonium oxidation. In an anammox enrichment culture fed with propionate for 150 days, the relative amounts of anammox cells and denitrifiers did not change significantly over time, indicating that anammox bacteria could compete successfully with heterotrophic denitrifiers for propionate. In conclusion, this study shows that anammox bacteria have a more versatile metabolism than previously assumed.     

Microbial diversity in arctic freshwaters is structured by inoculation of microbes from soils

Microbes are transported in hydrological networks through many environments, but the nature and dynamics of underlying microbial metacommunities and the impact of downslope inoculation on patterns of microbial diversity across landscapes are unknown. Pyrosequencing of small subunit ribosomal RNA gene hypervariable regions to characterize microbial communities along a hydrological continuum in arctic tundra showed a pattern of decreasing diversity downslope, with highest species richness in soil waters and headwater streams, and lowest richness in lake water. In a downstream lake, 58% and 43% of the bacterial and archaeal taxa, respectively, were also detected in diverse upslope communities, including most of the numerically dominant lake taxa. In contrast, only 18% of microbial eukaryotic taxa in the lake were detected upslope. We suggest that patterns of diversity in surface waters are structured by initial inoculation from microbial reservoirs in soils followed by a species-sorting process during downslope dispersal of both common and rare microbial taxa. Our results suggest that, unlike for metazoans, a substantial portion of bacterial and archaeal diversity in surface freshwaters may originate in complex soil environments.     

Intertwined effects of climate and land use change on environmental dynamics and carbon accumulation in a mangrove‐fringed coastal lagoon in Java,Indonesia

The identification and quantification of natural carbon (C) sinks is critical to global climate change mitigation efforts. Tropical coastal wetlands are considered important in this context, yet knowledge of their dynamics and quantitative data are still scarce. In order to quantify the C accumulation rate and understand how it is influenced by land use and climate change, a palaeoecological study was conducted in the mangrove‐fringed Segara Anakan Lagoon (SAL) in Java, Indonesia. A sediment core was age‐dated and analyzed for its pollen and spore, elemental and biogeochemical compositions. The results indicate that environmental dynamics in the SAL and its C accumulation over the past 400 years were controlled mainly by climate oscillations and anthropogenic activities. The interaction of these two factors changed the lagoon's sediment supply and salinity, which consequently altered the organic matter composition and deposition in the lagoon. Four phases with varying climates were identified. While autochthonous mangrove C was a significant contributor to carbon accumulation in SAL sediments throughout all four phases, varying admixtures of terrestrial C from the hinterland also contributed, with natural mixed forest C predominating in the early phases and agriculture soil C predominating in the later phases. In this context, climate‐related precipitation changes are an overarching control, as surface water transport through rivers serves as the “delivery agent” for the outcomes of the anthropogenic impact in the catchment area into the lagoon. Amongst mangrove‐dominated ecosystems globally, the SAL is one of the most effective C sinks due to high mangrove carbon input in combination with a high allochthonous carbon input from anthropogenically enhanced sediment from the hinterland and increased preservation. Given the substantial C sequestration capacity of the SAL and other mangrove‐fringed coastal lagoons, conservation and restoration of these ecosystems is vitally important for climate change mitigation.     

Soil anammox community structure in different land use soils treatment with 13 C urea as determined by analysis of phospholipid fatty acids

The anaerobic ammonium oxidation (anammox) process is globally an important nitrogen-cycling process mediated by specialized microbes. However, still little information is documented about anammox microbial community structure under agricultural soils. The anaerobic incubation experiment was conducted to study the impacts of different land use soils fertilized by 13C-urea on the activity and diversity of anammox bacteria using stable isotope to probe the phospholipid fatty acid (PLFA-SIP). The 13C was preferentially incorporated in ratios PLFAs 16:1ω7c, 16:1ω5c, and 16:0. The results revealed that the abundance of the anammox bacteria (both hzs-β and hzo) were observed in vegetable soil V1 and paddy soils (R1 and R2) means that they were positively correlated with 13C-urea but were negatively correlated with NO3 −-N and NH4 +-N concentrations. Thus, 13C-PLFAs 16:1ω7c, 16:1ω5c, and 16:0 could be the biomarker as soil anammox. The anaerobic microbial community composition of soils under different land use systems was diverse, and V1, R1, and R2 had similar microbial diversity and higher microbial biomass. The principal component analysis between soil properties and gene abundance suggested that not only pH but also soil organic matter, available P, and available K were important factors for the anammox process. This study suggested that 13C-Urea-PLFA for anaerobic incubation was a simple method to study anammox microbial community structure through affecting the soil nutrients, and the different land use systems played important roles in determining the microbial composition of soils.     

厌氧氨氧化与反硝化耦合反应研究进展

厌氧氨氧化是氮循环中一个重要的反应,对处理含高氨氮废水具有重大的潜在实际应用价值.高浓度有机碳源对厌氧氨氧化反应具有明显的抑制作用.如何在有机碳源存在的条件下实现厌氧氨氧化与反硝化的耦合,是实现厌氧氨氧化工程应用面临的巨大挑战.本文综述了有关厌氧氨氧化与反硝化耦合反应机理、反应功能性微生物种群、耦合工艺启动、过程调控及环境影响因素等的最新研究进展,并对厌氧氨氧化与反硝化耦合反应研究前景及其在废水处理中的应用进行了展望.     

厦门市重点保护植物空间优先保护格局研究

生物多样性保护对维持城市生态系统功能具有重要意义。以39种厦门市重点保护植物为对象,通过物种分布模型MaxENT获得物种潜在分布栅格图,利用空间保护优先化定量工具Zonation软件识别理论上既适宜重点保护植物生存又能够保证景观连通性的区域,获得本地重点保护植物景观保护等级。根据2020年全球生物多样性目标,将景观保护等级最高的17%区域视为多物种空间优先保护区,结合Zonation模型生成的随景观丧失物种加权灭绝风险曲线,将保护等级最高的8%区域划为一级保护区,保护等级在8%-17%范围内的区域划为二级保护区。利用MaxENT模型中的jackknife刀切法发现海拔是对本地重点保护植物分布影响最大的环境因子,优先保护区集中分布于海拔较低的海岸带区域。将优先保护区与自然保护地建设现状、厦门市生态功能区规划、土地利用规划、城市总体规划对比发现厦门市岛外西部、北部的优先保护区得到了较好保护;岛外的西南部及东南部、岛内的东部及南部海岸带的优先保护区被建设用地大规模占用,已纳入自然保护地范围的区域较少,存在大量的海岸带优先保护区保护空缺;岛外东南部的部分优先保护区虽未被占用,但规划中属发展备用地,缺乏生态保护。为避免优先保护区面积的进一步萎缩,应重点关注海岸带区域优先保护区的生态保护,将目前属于发展备用地的优先保护区转划为生态留白空间,针对一级、二级优先保护区分别实施刚性和弹性的生态保育措施,在保护生物多样性的同时,严控对海岸带区域优先保护区的进一步开发利用,协调优先保护区内保护与开发利用间的关系。     

Distinct taxonomic and functional composition of soil microbiomes along the gradient forest-restinga-mangrove in southeastern Brazil

Soil microorganisms play crucial roles in ecosystem functioning, and the central goal in microbial ecology studies is to elucidate which factors shape community structure. A better understanding of the relationship between microbial diversity, functions and environmental parameters would increase our ability to set conservation priorities. Here, the bacterial and archaeal community structure in Atlantic Forest, restinga and mangrove soils was described and compared based on shotgun metagenomics. We hypothesized that each distinct site would harbor a distinct taxonomic and functional soil community, which is influenced by environmental parameters. Our data showed that the microbiome is shaped by soil properties, with pH, base saturation, boron and iron content significantly correlated to overall community structure. When data of specific phyla were correlated to specific soil properties, we demonstrated that parameters such as boron, copper, sulfur, potassium and aluminum presented significant correlation with the most number of bacterial groups. Mangrove soil was the most distinct site and presented the highest taxonomic and functional diversity in comparison with forest and restinga soils. From the total 34 microbial phyla identified, 14 were overrepresented in mangrove soils, including several archaeal groups. Mangrove soils hosted a high abundance of sequences related to replication, survival and adaptation; forest soils included high numbers of sequences related to the metabolism of nutrients and other composts; while restinga soils included abundant genes related to the metabolism of carbohydrates. Overall, our finds show that the microbial community structure and functional potential were clearly different across the environmental gradient, followed by functional adaptation and both were related to the soil properties.     

高通量测序分析多种典型生境中厌氧氨氧化细菌的多样性分布特征

【背景】厌氧氨氧化过程是氮素循环过程的重要途径之一,在氮素循环中发挥重要作用。先前的研究已经证实了厌氧氨氧化细菌存在于多种生境中,但对其多样性分布还没有系统的研究。【目的】对厌氧氨氧化细菌在不同类型生境中的多样性分布规律进行深入分析,充分展示其在不同生境中的群落结构特点,并揭示多样性分布与环境因素之间的关系。【方法】在建立厌氧氨氧化细菌16S rRNA基因序列数据库的基础上,运用高通量测序技术分析其在不同生境中的多样性分布特征。【结果】厌氧氨氧化细菌在红树林、海湾和河口生境中的多样性水平较高,而污泥和红壤的多样性水平明显较低。系统发育分析表明,这些生境中的厌氧氨氧化细菌主要由Candidatus Brocadia、Ca.Scalindua和未明确分类地位的菌属组成;从河流到红树林生态系统,随着盐度的增加,厌氧氨氧化细菌的优势种属由Ca. Brocadia转变到Ca. Scalindua,相关性分析也表明了盐度是导致不同生境中厌氧氨氧化细菌群落结构差异的主要因素。【结论】不同生境中存在不同的厌氧氨氧化细菌种群结构,环境条件的差异影响了厌氧氨氧化细菌的种群分布和系统演化。     

Exploring the diversity of bacterial communities in sediments of urban mangrove forests

Municipal sewage, urban runoff and accidental oil spills are common sources of pollutants in urban mangrove forests and may have drastic effects on the microbial communities inhabiting the sediment. However, studies on microbial communities in the sediment of urban mangroves are largely lacking. In this study, we explored the diversity of bacterial communities in the sediment of three urban mangroves located in Guanabara Bay (Rio de Janeiro, Brazil). Analysis of sediment samples by means of denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments suggested that the overall bacterial diversity was not significantly affected by the different levels of hydrocarbon pollution at each sampling site. However, DGGE and sequence analyses provided evidences that each mangrove sediment displayed a specific structure bacterial community. Although primer sets for Pseudomonas, alphaproteobacterial and actinobacterial groups also amplified ribotypes belonging to taxa not intended to be enriched, sequence analyses of dominant DGGE bands revealed ribotypes related to Alteromonadales, Burkholderiales, Pseudomonadales, Rhodobacterales and Rhodocyclales. Members of these groups were often shown to be involved in aerobic or anaerobic degradation of hydrocarbon pollutants. Many of these sequences were only detected in the sampling sites with high levels of anthropogenic inputs of hydrocarbons. Many dominant DGGE ribotypes showed low levels of sequence identity to known sequences, indicating a large untapped bacterial diversity in mangrove ecosystems.