Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary

Ammonia oxidation in marine and estuarine sediments plays a pivotal role in the cycling and removal of nitrogen. Recent reports have shown that the newly discovered ammonia-oxidizing archaea can be both abundant and diverse in aquatic and terrestrial ecosystems. In this study, we examined the abundance and diversity of ammonia-oxidizing archaea (AOA) and betaproteobacteria (beta-AOB) across physicochemical gradients in San Francisco Bay--the largest estuary on the west coast of the USA. In contrast to reports that AOA are far more abundant than beta-AOB in both terrestrial and marine systems, our quantitative PCR estimates indicated that beta-AOB amoA (encoding ammonia monooxygenase subunit A) copy numbers were greater than AOA amoA in most of the estuary. Ammonia-oxidizing archaea were only more pervasive than beta-AOB in the low-salinity region of the estuary. Both AOA and beta-AOB communities exhibited distinct spatial structure within the estuary. AOA amoA sequences from the north part of the estuary formed a large and distinct low-salinity phylogenetic group. The majority of the beta-AOB sequences were closely related to other marine/estuarine Nitrosomonas-like and Nitrosospira-like sequences. Both ammonia-oxidizer community composition and abundance were strongly correlated with salinity. Ammonia-oxidizing enrichment cultures contained AOA and beta-AOB amoA sequences with high similarity to environmental sequences. Overall, this study significantly enhances our understanding of estuarine ammonia-oxidizing microbial communities and highlights the environmental conditions and niches under which different AOA and beta-AOB phylotypes may thrive.     

Abundance and diversity based on amoA genes of ammonia-oxidizing archaea and bacteria in ten wastewater treatment systems

The abundance and diversity of amoA genes of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were investigated in ten wastewater treatment systems (WTSs) by polymerase chain reaction (PCR), cloning, sequencing, and quantitative real-time PCR (qPCR). The ten WTSs included four full-scale municipal WTSs, three full-scale industrial WTSs, and three lab-scale WTSs. AOB were present in all the WTSs, whereas AOA were detected in nine WTSs. QPCR data showed that AOB amoA genes (4.625?×?10⁴–9.99?×?10⁹ copies g^?1 sludge) outnumbered AOA amoA genes (<limit of detection–1.90?×?10⁷ copies g^?1 sludge) in each WTS, indicating that AOB may play an important role than AOA in ammonia oxidization in WTSs. Interestingly, it was found that AOA and AOB coexisted with anaerobic ammonia oxidation (anammox) bacteria in three anammox WTSs with relatively higher abundance. In a full-scale industrial WTS where effluent ammonia was higher than influent ammonia, both AOA and AOB showed higher abundance. The phylogenetic analysis of AOB amoA genes showed that genera Nitrosomonas was the most dominant species in the ten WTSs; Nitrosomonas europaea cluster was the dominant major cluster, followed by Nitrosomonas-like cluster and Nitrosomonas oligotropha cluster; and AOB species showed higher diversity than AOA species. AOA were found to be affiliated with two major clusters: Nitrososphaera cluster and Nitrosopumilus cluster. Nitrososphaera cluster was the most dominant species in different samples and distributed worldwide.     

细菌与古菌之间的直接电子传递

冰川占地球陆地表面的11%,储存了约10⁴ Pg有机碳。随着冰川消融有机碳被释放至下游生态系统中,刺激海洋、湖泊和径流的初级生产力进而影响其生态系统。微生物参与的固碳过程决定了冰川有机碳储量及向下游输出碳量。研究冰川固碳微生物群落构成及其生态功能,可为估算冰川碳积累量和保护下游生态系统提供数据基础。本文综述了冰川碳储量和释放量、冰川生态系统主要固碳途径、固碳微生物群落组成、固碳速率以及影响固碳速率的环境因素。最后基于研究现状展望了冰川生态系统固碳微生物的未来研究和发展方向。     

Starch-hydrolyzing enzymes from thermophilic archaea and bacteria

Extremophlic microorganisms have developed a variety of molecular strategies in order to survive in harsh conditions. For the utilization of natural polymeric substrates such as starch, a number of extremophiles, belonging to different taxonomic groups, produce amylolytic enzymes. This class of enzyme is important not only for the study of biocatalysis and protein stability at extreme conditions but also for the many biotechnological opportunities they offer. In this review, we report on the different molecular properties of thermostable archaeal and bacterial enzymes including alpha-amylase, alpha-glucosidase, glucoamylase, pullulanase, and cyclodextrin glycosyltransferase. Comparison of the primary sequence of the pyrococcal pullulanase with other members of the glucosyl hydrolase family revealed that significant differences are responsible for the mode of action of these enzymes.     

FtsZ-less cell division in archaea and bacteria

A dedicated cell division machinery is needed for efficient proliferation of an organism. The eukaryotic actin-myosin based mechanism and the bacterial FtsZ-dependent machinery have both been characterized in detail, and a third division mechanism, the Cdv system, was recently discovered in archaea from the Crenarchaeota phylum. Despite these findings, division mechanisms remain to be identified in, for example, organisms belonging to the bacterial PVC superphylum, bacteria with extremely reduced genomes, wall-less archaea and bacteria, and in archaea that carry out the division process without cell constriction. Cytokinesis mechanisms in these clades and individual taxa are likely to include adaptation of host functions to division of bacterial symbionts, transfer of bacterial division genes into the host genome, vesicle formation without a dedicated constriction machinery, cross-wall formation without invagination, as well as entirely novel division mechanisms.     

Insertion sequence diversity in archaea.

Insertion sequences (ISs) can constitute an important component of prokaryotic (bacterial and archaeal) genomes. Over 1,500 individual ISs are included at present in the ISfinder database (www-is.biotoul.fr), and these represent only a small portion of those in the available prokaryotic genome sequences and those that are being discovered in ongoing sequencing projects. In spite of this diversity, the transposition mechanisms of only a few of these ubiquitous mobile genetic elements are known, and these are all restricted to those present in bacteria. This review presents an overview of ISs within the archaeal kingdom. We first provide a general historical summary of the known properties and behaviors of archaeal ISs. We then consider how transposition might be regulated in some cases by small antisense RNAs and by termination codon readthrough. This is followed by an extensive analysis of the IS content in the sequenced archaeal genomes present in the public databases as of June 2006, which provides an overview of their distribution among the major archaeal classes and species. We show that the diversity of archaeal ISs is very great and comparable to that of bacteria. We compare archaeal ISs to known bacterial ISs and find that most are clearly members of families first described for bacteria. Several cases of lateral gene transfer between bacteria and archaea are clearly documented, notably for methanogenic archaea. However, several archaeal ISs do not have bacterial equivalents but can be grouped into Archaea-specific groups or families. In addition to ISs, we identify and list nonautonomous IS-derived elements, such as miniature inverted-repeat transposable elements. Finally, we present a possible scenario for the evolutionary history of ISs in the Archaea.     

嗜盐菌耐盐机制相关基因的研究进展

嗜盐微生物能够在高盐环境中生存,其耐盐机制一直是微生物学家研究的热点。目前嗜盐微生物耐盐机制的研究主要集中在细胞吸K+排Na+作用、胞内积累小分子相容性溶质及嗜盐酶的氨基酸组成特性三个方面。文章从基因水平综述了嗜盐菌的耐盐机制,并对其在高盐废水处理上的应用进行讨论与展望。     

Membrane protein insertase YidC in bacteria and archaea

The insertion of proteins into the prokaryotic plasma membrane is catalyzed by translocases and insertases. On one hand, the Sec translocase operates as a transmembrane channel that can open laterally to first bind and then release the hydrophobic segments of a substrate protein into the lipid bilayer. On the other hand, YidC insertases interact with their substrates in a groove‐like structure at an amphiphilic protein–lipid interface thus allowing the transmembrane segments of the substrate to slide into the lipid bilayer. The recently published high‐resolution structures of YidC provide new mechanistic insights of how transmembrane proteins achieve the transition from an aqueous environment in the cytoplasm to the hydrophobic lipid bilayer environment of the membrane.     

Status of genome projects for nonpathogenic bacteria and archaea

Since the first microbial genome was sequenced in 1995, 30 others have been completed and an additional 99 are known to be in progress. Although the early emphasis of microbial genomics was on human pathogens for obvious reasons, a significant number of sequencing projects have focused on nonpathogenic organisms, beginning with the release of the complete genome sequence of the archaeon Methanococcus jannaschii in 1996. The past 18 months have seen the completion of the genomes of several unusual organisms, including Thermotoga maritima, whose genome reveals extensive potential lateral transfer with archaea; Deinococcus radiodurans, the most radiation-resistant microorganism known; and Aeropyrum pernix, the first Crenarchaeota to be completely sequenced. Although the functional characterization of genomic data is still in its initial stages, it is likely that microbial genomics will have a significant impact on environmental, food, and industrial biotechnology as well as on genomic medicine.     

Update of microbial genome programs for bacteria and archaea

Since the Haemophilus influenzae genome sequence was completed in 1995, 172 other prokaryotic genomes have been completely sequenced, while 508 projects are underway. Besides pathogens, organisms important in several other fields, such as biotechnology and bioremediation, have also been sequenced. Institutions choose the organisms they wish to sequence according to the importance that these species represent to them, the availability of the microbes, and based on the similarity of a species of interest with others that have been sequenced previously. Improvements in sequencing techniques and in associated methodologies have been achieved; however, scientists need to continue working on the development of this field. In Brazil, a multicentered, centrally coordinated and research-focused network was adopted and successfully used for the sequencing of several important organisms. We analyzed the current status of microbial genomes, the trends for criteria used to choose new sequencing projects, the future of microbial sequencing, and the Brazilian genome network.     

Ecophysiological characterization of ammonia-oxidizing archaea and bacteria from freshwater

Aerobic biological ammonia oxidation is carried out by two groups of microorganisms, ammonia-oxidizing bacteria (AOB) and the recently discovered ammonia-oxidizing archaea (AOA). Here we present a study using cultivation-based methods to investigate the differences in growth of three AOA cultures and one AOB culture enriched from freshwater environments. The strain in the enriched AOA culture belong to thaumarchaeal group I.1a, with the strain in one enrichment culture having the highest identity with "Candidatus Nitrosoarchaeum koreensis" and the strains in the other two representing a new genus of AOA. The AOB strain in the enrichment culture was also obtained from freshwater and had the highest identity to AOB from the Nitrosomonas oligotropha group (Nitrosomonas cluster 6a). We investigated the influence of ammonium, oxygen, pH, and light on the growth of AOA and AOB. The growth rates of the AOB increased with increasing ammonium concentrations, while the growth rates of the AOA decreased slightly. Increasing oxygen concentrations led to an increase in the growth rate of the AOB, while the growth rates of AOA were almost oxygen insensitive. Light exposure (white and blue wavelengths) inhibited the growth of AOA completely, and the AOA did not recover when transferred to the dark. AOB were also inhibited by blue light; however, growth recovered immediately after transfer to the dark. Our results show that the tested AOB have a competitive advantage over the tested AOA under most conditions investigated. Further experiments will elucidate the niches of AOA and AOB in more detail.     

Biodegradation of organic pollutants by halophilic bacteria and archaea

Hypersaline environments are important for both surface extension and ecological significance. As all other ecosystems, they are impacted by pollution. However, little information is available on the biodegradation of organic pollutants by halophilic microorganisms in such environments. In addition, it is estimated that 5% of industrial effluents are saline and hypersaline. Conventional nonextremophilic microorganisms are unable to efficiently perform the removal of organic pollutants at high salt concentrations. Halophilic microorganisms are metabolically different and are adapted to extreme salinity; these microorganisms are good candidates for the bioremediation of hypersaline environments and treatment of saline effluents. This literature survey indicates that both the moderately halophilic bacteria and the extremely halophilic archaea have a broader catabolic versatility and capability than previously thought. A diversity of contaminating compounds is susceptible to be degraded by halotolerant and halophile bacteria. Nevertheless, significant research efforts are still necessary in order to estimate the true potential of these microorganisms to be applied in environmental processes and in the remediation of contaminated hypersaline ecosystems. This effort should be also focused on basic research to understand the overall degradation mechanism, to identify the enzymes involved in the degradation process and the metabolism regulation.     

Review of ammonia-oxidizing bacteria and archaea in freshwater ponds

Aquaculture ponds are simple and unique ecosystems, which are affected intensively by human activities. In this mini-review, we focus our attention on the distribution and community diversity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in pond water and sediments, as well as the possible ecological mechanisms involved. Moreover, we discuss the possibility of increasing the activity of ammonia-oxidizing organisms in order to improve the water quality in aquaculture ponds. Compared with eutrophic lakes, the significantly higher ammonia concentration in pond water does not lead to significantly higher AOB levels, and the abundance of AOA is too low to quantify accurately. Similar to eutrophic lakes, high abundances of AOA and AOB are present in the surface sediments at the same time, where the oxidation of ammonia is performed mainly by AOB. AOB and AOA exhibit significant seasonal variations in aquaculture ponds, which are affected by the temperature, pH, and dissolved oxygen. The dominant AOB species are Nitrosomonas and the Nitrosospira lineage in pond environments. Nitrososphaera or members of the Nitrososphaera-like cluster dominate the AOA species in surface sediments, whereas the Nitrosopumilus cluster dominates the deeper sediments. AOB and AOA can be enriched on artificial substrates suspended in the pond water, thereby potentially improving the water quality.