Chitinase gene sequences retrieved from diverse aquatic habitats reveal environment-specific distributions

Perspectives on Expanding the Repertoire of Novel Microbial Chitinases for Biological Control

Interest in chitin-degrading enzymes has grown over the years, and microbial chitinases are the most attractive and promising candidates for the control of plant pests (fungi and insects). Currently, there are many studies on chitinases produced by cultivable microorganisms; however, almost none of them have achieved acceptable applicability as a biopesticide in the field. Approximately 99% of the microorganisms from soil cannot be isolated by conventional culture-dependent methods, thus having an enormous biotechnological/genetic potential to be explored. On the basis of this, the present paper aims to provide a brief overview of the metagenomic opportunities that have been emerging and allowing access to the biochemical potential of uncultivable microorganisms through the direct mining of DNA sequences recovered from the environment. This work also shortly discussed the future perspectives of functional and sequence-based metagenomic approaches for the identification of new chitinase-coding genes with potential for applications in several agricultural and biotechnological industries, especially in biological control.

Shifts in the Microbial Community of Activated Sludge with Different COD/N Ratios or Dissolved Oxygen Levels in Tibet, China

In this study, we examined the influence of the organic carbon-to-nitrogen ratio (chemical oxygen demand (COD/N)) and dissolved oxygen (DO) levels on the removal efficiency of pollutants and on the change in total microflora in the cyclic activated sludge system (CASS) in the Nyingchi prefecture in Tibet. The results demonstrated that the treatment performance was the best when the COD/N ratio was 7:1 or the DO levels were 2–2.5 mg/L in comparison with four different tested COD/N ratios (4:1, 5:1, 7:1, and 10:1) and DO concentrations (0.5–1, 1–2, 2–2.5, and 2.5–3.5 mg/L). The treatment performance can be explained by the relative operational taxonomic unit richness and evenness of the microbial communities in activated sludge. Evident microbial variance was observed, especially different COD/N ratios and DO concentrations, which were conducive to the disposal of urban sewage in plateaus. The results help to understand sewage treatment under different COD/N ratios or DO concentrations on plateaus. This work provides practical guidance for the operation of any wastewater treatment plant on a plateau.

Antarctic Krill Are Reservoirs for Distinct Southern Ocean Microbial Communities

Host-associated bacterial communities have received limited attention in polar habitats, but are likely to represent distinct nutrient-rich niches compared to the surrounding environment. Antarctic krill (Euphausia superba) are a super-abundant species with a circumpolar distribution, and the krill microbiome may make a substantial contribution to marine bacterial diversity in the Southern Ocean. We used high-throughput sequencing of the bacterial 16S ribosomal RNA gene to characterize bacterial diversity in seawater and krill tissue samples from four locations south of the Kerguelen Plateau, one of the most productive regions in the Indian Sector of the Southern Ocean. Krill-associated bacterial communities were distinct from those of the surrounding seawater, with different communities inhabiting the moults, digestive tract and faecal pellets, including several phyla not detected in the surrounding seawater. Digestive tissues from many individuals contained a potential gut symbiont (order: Mycoplasmoidales) shown to improve survival on a low quality diet in other crustaceans. Antarctic krill swarms thus influence Southern Ocean microbial communities not only through top-down grazing of eukaryotic cells and release of nutrients into the water column, but also by transporting distinct microbial assemblages horizontally via migration and vertically via sinking faecal pellets and moulted exuviae. Changes to Antarctic krill demographics or distribution through fishing pressure or climate-induced range shifts will also influence the composition and dispersal of Southern Ocean microbial communities.

Organic carbon source and salinity shape sediment bacterial composition in two China marginal seas and their major tributaries

Marginal sea sediments receive organic substrates of different origins, but whether and to what extent sediment microbial communities are reflective of the different sources of organic substrates remain unclear. To address these questions, sediment samples were collected in two connected China marginal seas, i.e., Bohai Sea and Yellow Sea, and their two major tributaries (Yellow River and Liao River). Sediment bacterial community composition (BCC) was examined using 16S rRNA gene pyrosequencing. In addition, physicochemical variables that describe environmental conditions and sediment features were measured. Our results revealed that BCCs changed with salinity and organic carbon (OC) content. Members of Gaiellaceae and Comamonadaceae showed a rapid decrease as salinity and phytoplankton-derived OC increased, while Piscirickettsiaceae and Desulfobulbaceae exhibited an opposite distribution pattern. Differences of riverine vs. marginal sea sediment BCCs could be mostly explained by salinity. However, within the marginal seas, sediment BCC variations were mainly explained by OC-related variables, including terrestrial-derived fatty acids (Terr_FA), phytoplankton-derived polyunsaturated fatty acids (Phyto_PUFA), stable carbon isotopes (δ¹³C), and carbon to nitrogen ratio (C/N). In addition to environmental variables, network analysis suggested that interactions among individual bacterial taxa might be important in shaping sediment BCCs in the studied areas.

Composition and Activity of Microbial Communities along the Redox Gradient of an Alkaline, Hypersaline, Lake

We compared the composition of microbial communities obtained by sequencing 16S rRNA gene amplicons with taxonomy derived from metatranscriptomes from the same samples. Samples were collected from alkaline, hypersaline Mono Lake, California, USA at five depths that captured the major redox zones of the lake during the onset of meromixis. The prokaryotic community was dominated by bacteria from the phyla Proteobacteria, Firmicutes, and Bacteroidetes, while the picoeukaryotic chlorophyte Picocystis dominated the eukaryotes. Most (80%) of the abundant (>1% relative abundance) OTUs recovered as amplicons of 16S rRNA genes have been reported in previous surveys, indicating that Mono Lake's microbial community has remained stable over 12 years that have included periods of regular, annual overturn interspersed by episodes of prolonged meromixis that result in extremely reducing conditions in bottom water. Metatranscriptomic sequences binned predominately to the Gammaproteobacteria genera Thioalkalivibrio (4–13%) and Thioalkalimicrobium (0–14%); and to the Firmicutes genera Dethiobacter (0–5%) and Clostridium (1–4%), which were also abundant in the 16S rRNA gene amplicon libraries. This study provides insight into the taxonomic affiliations of transcriptionally active communities of the lake's water column under different redox conditions.

Production and characterization of a novel antifungal chitinase identified by functional screening of a suppressive-soil metagenome

Background

Through functional screening of a fosmid library, generated from a phytopathogen-suppressive soil metagenome, the novel antifungal chitinase—named Chi18H8 and belonging to family 18 glycosyl hydrolases—was previously discovered. The initial extremely low yield of Chi18H8 recombinant production and purification from Escherichia coli cells (21 μg/g cell) limited its characterization, thus preventing further investigation on its biotechnological potential.

Results

We report on how we succeeded in producing hundreds of milligrams of pure and biologically active Chi18H8 by developing and scaling up to a high-yielding, 30 L bioreactor process, based on a novel method of mild solubilization of E. coli inclusion bodies in lactic acid aqueous solution, coupled with a single step purification by hydrophobic interaction chromatography. Chi18H8 was characterized as a Ca²⁺-dependent mesophilic chitobiosidase, active on chitin substrates at acidic pHs and possessing interesting features, such as solvent tolerance, long-term stability in acidic environment and antifungal activity against the phytopathogens Fusarium graminearum and Rhizoctonia solani. Additionally, Chi18H8 was found to operate according to a non-processive endomode of action on a water-soluble chitin-like substrate.

Conclusions

Expression screening of a metagenomic library may allow access to the functional diversity of uncultivable microbiota and to the discovery of novel enzymes useful for biotechnological applications. A persisting bottleneck, however, is the lack of methods for large scale production of metagenome-sourced enzymes from genes of unknown origin in the commonly used microbial hosts. To our knowledge, this is the first report on a novel metagenome-sourced enzyme produced in hundreds-of-milligram amount by recovering the protein in the biologically active form from recombinant E. coli inclusion bodies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-017-0634-8) contains supplementary material, which is available to authorized users.

Metagenomics-Guided Mining of Commercially Useful Biocatalysts from Marine Microorganisms

Marine microorganisms are a rich reservoir of highly diverse and unique biocatalysts that offer potential applications in food, pharmaceutical, fuel, and cosmetic industries. The fact that only less than 1% of microbes in any marine habitats can be cultured under standard laboratory conditions has hampered access to their extraordinary biocatalytic potential. Metagenomics has recently emerged as a powerful and well-established tool to investigate the vast majority of hidden uncultured microbial diversity for the discovery of novel industrially relevant enzymes from different types of environmental samples, such as seawater, marine sediment, and symbiotic microbial consortia. We discuss here in this review about approaches and methods in metagenomics that have been used and can potentially be used to mine commercially useful biocatalysts from uncultured marine microbes.

Integrated (Meta) Genomic and Synthetic Biology Approaches to Develop New Biocatalysts

In recent years, the marine environment has been the subject of increasing attention from biotechnological and pharmaceutical industries as a valuable and promising source of novel bioactive compounds. Marine biodiscovery programmes have begun to reveal the extent of novel compounds encoded within the enormous bacterial richness and diversity of the marine ecosystem. A combination of unique physicochemical properties and spatial niche-specific substrates, in wide-ranging and extreme habitats, underscores the potential of the marine environment to deliver on functionally novel biocatalytic activities. With the growing need for green alternatives to industrial processes, and the unique transformations which nature is capable of performing, marine biocatalysts have the potential to markedly improve current industrial pipelines. Furthermore, biocatalysts are known to possess chiral selectivity and specificity, a key focus of pharmaceutical drug design. In this review, we discuss how the explosion in genomics based sequence analysis, allied with parallel developments in synthetic and molecular biology, have the potential to fast-track the discovery and subsequent improvement of a new generation of marine biocatalysts.

Chitin and Products of Its Hydrolysis in Vibrio cholerae Ecology

The role of chitin and its hydrolysis products generated by Vibrio cholerae chitinases in mechanisms of its adaptation in water environments, metabolism, preservation, acquisition of pathogenic potential, and its epidemiological value are reviewed. Chitin utilization by V. cholerae as a source of energy, carbon, and nitrogen is described. Chitin association promotes biofilm formation on natural chitinous surfaces, increasing V. cholerae resistance to adverse factors in ecological niches: the human body and water environments with its inhabitants. Hydrolytic enzymes regulated by the corresponding genes result in complete chitin biodegradation by a chitinolytic catabolic cascade. Consequences of V. cholerae cell and chitin interaction at different hierarchical levels include metabolic and physiological cell reactions such as chemotaxis, cell division, biofilm formation, induction of genetic competence, and commensalic and symbiotic mutual relations with higher organisms, nutrient cycle, pathogenicity for humans, and water organisms that is an example of successful interrelation of bacteria and substratum in the ecology of the microorganism.

Pilot-scale chitin extraction from shrimp shell waste by deproteination and decalcification with bacterial enrichment cultures

Extraction of chitin from mechanically pre-purified shrimp shells can be achieved by successive NaOH/HCl treatment, protease/HCl treatment or by environmentally friendly fermentation with proteolytic/lactic acid bacteria (LAB). For the last mentioned alternative, scale-up of shrimp shell chitin purification was investigated in 0.25 L (F1), 10 L (F2), and 300 L (F3) fermenters using an anaerobic, chitinase-deficient, proteolytic enrichment culture from ground meat for deproteination and a mixed culture of LAB from bio-yoghurt for decalcification. Protein removal in F1, F2, and F3 proceeded in parallel within 40 h at an efficiency of 89-91 %. Between 85 and 90 % of the calcit was removed from the shells by LAB in another 40 h in F1, F2, and F3. After deproteination of shrimp shells in F3, spent fermentation liquor was re-used for a next batch of 30-kg shrimp shells in F4 (300 L) which eliminated 85.5 % protein. The purity of the resulting chitin was comparable in F1, F2, F3, and F4. Viscosities of chitosan, obtained after chitin deacetylation and of chitin, prepared biologically or chemically in the laboratory, were much higher than those of commercially available chitin and chitosan.

Bacterial chitinase with phytopathogen control capacity from suppressive soil revealed by functional metagenomics

Plant disease caused by fungal pathogens results in vast crop damage globally. Microbial communities of soil that is suppressive to fungal crop disease provide a source for the identification of novel enzymes functioning as bioshields against plant pathogens. In this study, we targeted chitin-degrading enzymes of the uncultured bacterial community through a functional metagenomics approach, using a fosmid library of a suppressive soil metagenome. We identified a novel bacterial chitinase, Chi18H8, with antifungal activity against several important crop pathogens. Sequence analyses show that the chi18H8 gene encodes a 425-amino acid protein of 46 kDa with an N-terminal signal peptide, a catalytic domain with the conserved active site F¹⁷⁵DGIDIDWE¹⁸³, and a chitinase insertion domain. Chi18H8 was expressed (pGEX-6P-3 vector) in Escherichia coli and purified. Enzyme characterization shows that Chi18H8 has a prevalent chitobiosidase activity with a maximum activity at 35 °C at pH lower than 6, suggesting a role as exochitinase on native chitin. To our knowledge, Chi18H8 is the first chitinase isolated from a metagenome library obtained in pure form and which has the potential to be used as a candidate agent for controlling fungal crop diseases. Furthermore, Chi18H8 may also answer to the demand for novel chitin-degrading enzymes for a broad range of other industrial processes and medical purposes.

Shifts in microbial community in response to dissolved oxygen levels in activated sludge

This study evaluates the degradative efficiency of activated biomass collected from a Common Effluent Treatment Plant (CETP) under three different dissolved oxygen (DO) levels, 1, 2 and 4mgl(-1). The change in bacterial diversity with reference to DO levels was also analyzed. Results demonstrate that degradative efficiency was the highest, when the reactor was maintained at 4mgl(-1) DO, but amplicon library analysis showed a greater diversity of bacteria in the reactor maintained at 2mgl(-1) DO. Bacteria belonging to the order Desulfuromonadales, Entomoplasmatales, Pasteurellales, Thermales and Chloroflexales have only been detected in this reactor. Ammonia and nitrate levels in all three reactors indicated efficient nitrification process. Results of this study offer new insights into understanding the performance of activated biomass vis-à-vis microbial diversity and degradative efficiency with reference to DO. This information would be useful in improving the efficiency of any wastewater treatment plant.

Vogel T, Simonet P. Soil bacterial community shifts after chitin enrichment: an integrative metagenomic approach

Chitin is the second most produced biopolymer on Earth after cellulose. Chitin degrading enzymes are promising but untapped sources for developing novel industrial biocatalysts. Hidden amongst uncultivated micro-organisms, new bacterial enzymes can be discovered and exploited by metagenomic approaches through extensive cloning and screening. Enrichment is also a well-known strategy, as it allows selection of organisms adapted to feed on a specific compound. In this study, we investigated how the soil bacterial community responded to chitin enrichment in a microcosm experiment. An integrative metagenomic approach coupling phylochips and high throughput shotgun pyrosequencing was established in order to assess the taxonomical and functional changes in the soil bacterial community. Results indicate that chitin enrichment leads to an increase of Actinobacteria, γ-proteobacteria and β-proteobacteria suggesting specific selection of chitin degrading bacteria belonging to these classes. Part of enriched bacterial genera were not yet reported to be involved in chitin degradation, like the members from the Micrococcineae sub-order (Actinobacteria). An increase of the observed bacterial diversity was noticed, with detection of specific genera only in chitin treated conditions. The relative proportion of metagenomic sequences related to chitin degradation was significantly increased, even if it represents only a tiny fraction of the sequence diversity found in a soil metagenome.

Psychrotolerant antifungal Streptomyces isolated from Tawang, India and the shift in chitinase gene family

A total of 210 Streptomyces were isolated from the soil samples of Tawang, India where temperature varied from 5 °C during daytime to -2 °C during the night. Based on antifungal activity, a total of 33 strains, putatively Streptomyces spp., were selected. Optimal growth temperature for the 33 strains was 16 °C, with growth occurring down to 6 °C but not above 30 °C. Phylogenetic analysis based on 16S rDNA sequences revealed the taxonomic affiliation of the 33 strains as species of Streptomyces. To examine the relatedness of the chitinase genes from six strong antifungal Streptomyces strains, a phylogenetic tree was constructed using the catalytic domain nucleotide sequences and resulted in seven distinct monophyletic groups. A quantitative PCR study for chitinase expressing ability revealed that of the six antifungal strains tested, the strain Streptomyces roseochromogenus TSR12 was the most active producer of family 18 chitinase genes. Streptomyces strains with enhanced inhibitory potential usually encode a family 19 chitinase gene; however, our present study did not show expression of this family in the six strains tested.

Mining of unexplored habitats for novel chitinases--chiA as a helper gene proxy in metagenomics

The main objective of this study was to assess the abundance and diversity of chitin-degrading microbial communities in ten terrestrial and aquatic habitats in order to provide guidance to the subsequent exploration of such environments for novel chitinolytic enzymes. A combined protocol which encompassed (1) classical overall enzymatic assays, (2) chiA gene abundance measurement by qPCR, (3) chiA gene pyrosequencing, and (4) chiA gene-based PCR-DGGE was used. The chiA gene pyrosequencing is unprecedented, as it is the first massive parallel sequencing of this gene. The data obtained showed the existence across habitats of core bacterial communities responsible for chitin assimilation irrespective of ecosystem origin. Conversely, there were habitat-specific differences. In addition, a suite of sequences were obtained that are as yet unregistered in the chitinase database. In terms of chiA gene abundance and diversity, typical low-abundance/diversity versus high-abundance/diversity habitats was distinguished. From the combined data, we selected chitin-amended agricultural soil, the rhizosphere of the Arctic plant Oxyria digyna and the freshwater sponge Ephydatia fluviatilis as the most promising habitats for subsequent bioexploration. Thus, the screening strategy used is proposed as a guide for further metagenomics-based exploration of the selected habitats.

An expansion of age constraints for microbial clades that lack a conventional fossil record using phylogenomic dating

Most microbial taxa lack a conventional microfossil or biomarker record, and so we currently have little information regarding how old most microbial clades and their associated traits are. Building on the previously published oxygen age constraint, two new age constraints are proposed based on the ability of microbial clades to metabolize chitin and aromatic compounds derived from lignin. Using the archaeal domain of life as a test case, phylogenetic analyses, along with published metabolic and genetic data, showed that members of the Halobacteriales and Thermococcales are able to metabolize chitin. Ancestral state reconstruction combined with phylogenetic analysis of the genes underlying chitin degradation predicted that the ancestors of these two groups were also likely able to metabolize chitin or chitin-related compounds. These two clades were therefore assigned a maximum age of 1.0 Ga (when chitin likely first appeared). Similar analyses also predicted that the ancestor to the Sulfolobus solfataricus-Sulfolobus islandicus clade was able to metabolize phenol using catechol dioxygenase, so this clade was assigned a maximum age of 475 Ma. Inferred ages of archaeal clades using relaxed molecular clocks with the new age constraints were consistent with those inferred with the oxygen age constraints. This work expands our current toolkit to include Paleoproterozoic, Neoproterozoic, and Paleozoic age constraints, and should aid in our ability to phylogenetically reconstruct the antiquity of a wide array of microbial clades and their associated morphological and biogeochemical traits, spanning deep geologic time. Such hypotheses-although built upon evolutionary inferences-are fundamentally testable.

Bacterial chitin hydrolysis in two lakes with contrasting trophic statuses

Chitin, which is a biopolymer of the amino sugar glucosamine (GlcN), is highly abundant in aquatic ecosystems, and its degradation is assigned a key role in the recycling of carbon and nitrogen. In order to study the significance of chitin decomposition in two temperate freshwater lakes with contrasting trophic and redox conditions, we measured the turnover rate of the chitin analog methylumbelliferyl-N,N'-diacetylchitobioside (MUF-DC) and the presence of chitinase (chiA) genes in zooplankton, water, and sediment samples. In contrast to the eutrophic and partially anoxic lake, chiA gene fragments were detectable throughout the oligotrophic water column and chiA copy numbers per ml of water were up to 15 times higher than in the eutrophic waters. For both lakes, the highest chiA abundance was found in the euphotic zone--the main habitat of zooplankton, but also the site of production of easily degradable algal chitin. The bulk of chitinase activity was measured in zooplankton samples and the sediments, where recalcitrant chitin is deposited. Both, chiA abundance and chitinase activity correlated well with organic carbon, nitrogen, and concentrations of particulate GlcN. Our findings show that chitin, although its overall contribution to the total organic carbon is small (~0.01 to 0.1%), constitutes an important microbial growth substrate in these temperate freshwater lakes, particularly where other easily degradable carbon sources are scarce.

Analysis of bacterial and archaeal diversity in coastal microbial mats using massive parallel 16S rRNA gene tag sequencing

Coastal microbial mats are small-scale and largely closed ecosystems in which a plethora of different functional groups of microorganisms are responsible for the biogeochemical cycling of the elements. Coastal microbial mats play an important role in coastal protection and morphodynamics through stabilization of the sediments and by initiating the development of salt-marshes. Little is known about the bacterial and especially archaeal diversity and how it contributes to the ecological functioning of coastal microbial mats. Here, we analyzed three different types of coastal microbial mats that are located along a tidal gradient and can be characterized as marine (ST2), brackish (ST3) and freshwater (ST3) systems. The mats were sampled during three different seasons and subjected to massive parallel tag sequencing of the V6 region of the 16S rRNA genes of Bacteria and Archaea. Sequence analysis revealed that the mats are among the most diverse marine ecosystems studied so far and consist of several novel taxonomic levels ranging from classes to species. The diversity between the different mat types was far more pronounced than the changes between the different seasons at one location. The archaeal community for these mats have not been studied before and revealed a strong reaction on a short period of draught during summer resulting in a massive increase in halobacterial sequences, whereas the bacterial community was barely affected. We concluded that the community composition and the microbial diversity were intrinsic of the mat type and depend on the location along the tidal gradient indicating a relation with salinity.

The importance of chitin in the marine environment

Chitin is the most abundant renewable polymer in the oceans and is an important source of carbon and nitrogen for marine organisms. The process of chitin degradation is a key step in the cycling of nutrients in the oceans and chitinolytic bacteria play a significant role in this process. These bacteria are autochthonous to both marine and freshwater ecosystems and produce chitinases that degrade chitin, an insoluble polysaccharide, to a biologically useful form. In this brief review, a description of the structure of chitin and diversity of chitinolytic bacteria in the oceans is provided, in the context of the significance of chitin degradation for marine life.

Novel chitinase genes from metagenomic DNA prepared from marine sediments in southwest Japan

Chitinase degrades chitin which comprises an important source of carbon and nitrogen in the marine environment. The aim of this study was to evaluate the population of chitinases in the marine sediments in southwest Japan. We collected marine sediments from eutrophic inner bay and offshore. Chitin-degrading bacteria were enriched from both sediments. Metagenomic DNA was isolated from the enriched chitin-degrading bacterial cell culture. At the same time, 25 chitin-degrading bacteria were isolated from the enriched culture. Partial fragments of chitinase genes were successfully amplified with degenerate primers designed for the glycoside hydrolase 18 family. We analyzed chitinase gene sequences of about 500 clones from metagenomic DNA prepared from chitin-degrading bacteria. Based on translated amino acid sequences, chitinases were grouped into five groups. Chitinases in groups II and III was most abundant and close to chitinase genes of several species of proteobacteria. On the other hand, chitinases in groups I, IV and V were unique and distinct from the known chitinases. These results indicate that the marine sediments used in this study contain diversity of chitinase genes.

Comprehensive approaches to molecular biomarker discovery for detection and identification of Cronobacter spp. (Enterobacter sakazakii) and Salmonella spp

Cronobacter spp. (formerly Enterobacter sakazakii) and Salmonella spp. are increasingly implicated internationally as important microbiological contaminants in low-moisture food products, including powdered infant formula. Estimates indicate that 40 to 80% of infants infected with Cronobacter sakazakii and/or Salmonella in the United States may not survive the illness. A systematic approach, combining literature-based data mining, comparative genome analysis, and the direct sequencing of PCR products of specific biomarker genes, was used to construct an initial collection of genes to be targeted. These targeted genes, particularly genes encoding virulence factors and genes responsible for unique phenotypes, have the potential to function as biomarker genes for the identification and differentiation of Cronobacter spp. and Salmonella from other food-borne pathogens in low-moisture food products. In this paper, a total of 58 unique Salmonella gene clusters and 126 unique potential Cronobacter biomarkers and putative virulence factors were identified. A chitinase gene, a well-studied virulence factor in fungi, plants, and bacteria, was used to confirm this approach. We found that the chitinase gene has very low sequence variability and/or polymorphism among Cronobacter, Citrobacter, and Salmonella, while differing significantly in other food-borne pathogens, either by sequence blasting or experimental testing, including PCR amplification and direct sequencing. This computational analysis for Cronobacter and Salmonella biomarker identification and the preliminary laboratory studies are only a starting point; thus, PCR and array-based biomarker verification studies of these and other food-borne pathogens are currently being conducted.

Microbial extracellular enzymes and the marine carbon cycle

Extracellular enzymes initiate microbial remineralization of organic matter by hydrolyzing substrates to sizes sufficiently small to be transported across cell membranes. As much of marine primary productivity is processed by heterotrophic microbes, the substrate specificities of extracellular enzymes, the rates at which they function in seawater and sediments, and factors controlling their production, distribution, and active lifetimes, are central to carbon cycling in marine systems. In this review, these topics are considered from biochemical, microbial/molecular biological, and geochemical perspectives. Our understanding of the capabilities and limitations of heterotrophic microbial communities has been greatly advanced in recent years, in part through genetic and genomic approaches. New methods to measure enzyme activities in the field are needed to keep pace with these advances and to pursue intriguing evidence that patterns of enzyme activities in different environments are linked to differences in microbial community composition that may profoundly affect the marine carbon cycle.

Expression and characterization of a novel mesophilic protease from metagenomic library derived from Antarctic coastal sediment

A metagenomic cosmid library was constructed, in which the insert DNA was derived from the coastal sediment near Antarctic China Zhongshan Station. One clone (ACPRO001) expressing protease activity was isolated from the library using milk agar plates. Sequencing of the clone revealed a novel protease gene. The amino acid sequence comparison and phylogenetic analysis indicated that it could be classified as a subtilisin-like serine protease, though the highly conserved residue Asp was replaced by Ala. The ACPRO001 protease gene was expressed in pET-His and purified for characterization. The optimal temperature and pH for the activity of the ACPRO001 protease were 60°C and pH 9.0, respectively. The enzyme retained about 73% of residual activity after 2 h incubation at 50°C in the presence of Ca(2+). The presence of Ca(2+) increased the thermostability of ACPRO001 protease obviously. The enzymatic activity was inhibited by 1 mM phenylmethyl sulfonylfluoride (PMSF) and hydrochloride 4-(2-aminoethyl)-benzenesulfonyl fluoride (AEBSF), indicating that it was a serine protease.

Molecular detection and diversity of xylanase genes in alpine tundra soil

Xylan is a major polysaccharide in plant cell walls, and its degradation is mainly conducted by microbial xylanases in nature. To explore the xylanase diversity in the environment, two sets of degenerate primers were designed based on the microbial xylanase sequences in Pfam database of glycosyl hydrolase (GH) family 10 and 11 and were used to amplify objective gene fragments directly from the alpine tundra soil DNA of the Tianshan Mountains, China. Ninety-six distinct GH 10 and 31 GH 11 xylanase gene fragments were retrieved, and most of them have low identities with known sequences in GenBank. Based on phylogenetic analysis, all of the GH 10 xylanase sequences fell into six clusters and were related to xylanases from Actinobacteria, Proteobacteria, Verrucomicrobia, Bacteroidetes, Firmicutes, and Acidobacteria. Three clusters of GH 11 xylanase sequences were established, and two of them were related with enzymes from fungi. These results indicated the diversity of xylanase genes in this cold environment. Four xylanolytic strains were isolated from the soil, and GH 10 xylanase gene fragments were cloned using the same primers. A full-length gene was obtained and expressed in Escherichia coli, and the recombinant enzyme showed some cold-related characteristics. Our study provides an efficient molecular approach to study xylanase in complex environments and casts an insight into the diversity and distribution of xylanases in a cold environment, which is very meaningful to understand their roles in xylan degradation in nature.

Expression of acetate permease-like (apl ) genes in subsurface communities of Geobacter species under fluctuating acetate concentrations

The addition of acetate to uranium-contaminated aquifers in order to stimulate the growth and activity of Geobacter species that reduce uranium is a promising in situ bioremediation option. Optimizing this bioremediation strategy requires that sufficient acetate be added to promote Geobacter species growth. We hypothesized that under acetate-limiting conditions, subsurface Geobacter species would increase the expression of either putative acetate symporters genes (aplI and aplII). Acetate was added to a uranium-contaminated aquifer (Rifle, CO) in two continuous amendments separated by 5 days of groundwater flush to create changing acetate concentrations. While the expression of aplI in monitoring well D04 (high acetate) weakly correlated with the acetate concentration over time, the transcript levels for this gene were relatively constant in well D08 (low acetate). At the lowest acetate concentrations during the groundwater flush, the transcript levels of aplII were the highest. The expression of aplII decreased 2-10-fold upon acetate reintroduction. However, the overall instability of acetate concentrations throughout the experiment could not support a robust conclusion regarding the role of apl genes in response to acetate limitation under field conditions, in contrast to previous chemostat studies, suggesting that the function of a microbial community cannot be inferred based on lab experiments alone.

Functional prokaryotic RubisCO from an oceanic metagenomic library

Culture-independent studies have indicated that there is significant diversity in the ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) enzymes used by marine, freshwater, and terrestrial autotrophic bacteria. Surprisingly, little is known about the catalytic properties of many environmentally significant RubisCO enzymes. Because one of the goals of RubisCO research is to somehow modify or select for RubisCO molecules with improved kinetic properties, a facile means to isolate functional and novel RubisCO molecules directly from the environment was developed. In this report, we describe the first example of functional RubisCO proteins obtained from genes cloned and characterized from metagenomic libraries derived from DNA isolated from environmental samples. Two form IA marine RubisCO genes were cloned, and each gene supported both photoheterotrophic and photoautotrophic growth of a RubisCO deletion strain of Rhodobacter capsulatus, strain SBI/II(-), indicating that catalytically active recombinant RubisCO was synthesized. The catalytic properties of the metagenomic RubisCO molecules were further characterized. These experiments demonstrated the feasibility of studying the functional diversity and enzymatic properties of RubisCO enzymes without first cultivating the host organisms. Further, this "proof of concept" experiment opens the way for development of a simple functional screen to examine the properties of diverse RubisCO genes isolated from any environment, and subsequent further bioselection may be possible if the growth conditions of complemented R. capsulatus strain SBI/II(-) are varied.

Approaches for novel enzyme discovery from marine environments

The enormous pool of biodiversity in marine ecosystems is an excellent natural reservoir for acquiring an inventory of enzymes with potential for biotechnological applications. Moreover, the opportunity for sustainable resource management has been greatly enhanced by recent advances in culturing methods for recalcitrant microbes. In this review, we will focus primarily on successful examples in culturing marine microbes and provide an overview of work examining the biotechnological potential of the marine reservoir, mainly through genomic strategies, such as activity-based functional screening of genomic and metagenomic libraries and homology-driven screening of enormous amounts of sequence data.

Chitinase genes revealed and compared in bacterial isolates, DNA extracts and a metagenomic library from a phytopathogen-suppressive soil

Soil that is suppressive to disease caused by fungal pathogens is an interesting source to target for novel chitinases that might be contributing towards disease suppression. In this study, we screened for chitinase genes, in a phytopathogen-suppressive soil in three ways: (1) from a metagenomic library constructed from microbial cells extracted from soil, (2) from directly extracted DNA and (3) from bacterial isolates with antifungal and chitinase activities. Terminal restriction fragment length polymorphism (T-RFLP) of chitinase genes revealed differences in amplified chitinase genes from the metagenomic library and the directly extracted DNA, but approximately 40% of the identified chitinase terminal restriction fragments (TRFs) were found in both sources. All of the chitinase TRFs from the isolates were matched to TRFs in the directly extracted DNA and the metagenomic library. The most abundant chitinase TRF in the soil DNA and the metagenomic library corresponded to the TRF(103) of the isolate Streptomyces mutomycini and/or Streptomyces clavifer. There were good matches between T-RFLP profiles of chitinase gene fragments obtained from different sources of DNA. However, there were also differences in both the chitinase and the 16S rRNA gene T-RFLP patterns depending on the source of DNA, emphasizing the lack of complete coverage of the gene diversity by any of the approaches used.

Probiotics and gastrointestinal disease: successes, problems and future prospects

Gastrointestinal disease is a major cause of morbidity and mortality worldwide each year. Treatment of chronic inflammatory gastrointestinal conditions such as ulcerative colitis and Crohn's disease is difficult due to the ambiguity surrounding their precise aetiology. Infectious gastrointestinal diseases, such as various types of diarrheal disease are also becoming increasingly difficult to treat due to the increasing dissemination of antibiotic resistance among microorganisms and the emergence of the so-called 'superbugs'. Taking into consideration these problems, the need for novel therapeutics is essential. Although described for over a century probiotics have only been extensively researched in recent years. Their use in the treatment and prevention of disease, particularly gastrointestinal disease, has yielded many successful results, some of which we outline in this review. Although promising, many probiotics are hindered by inherent physiological and technological weaknesses and often the most clinically promising strains are unusable. Consequently we discuss various strategies whereby probiotics may be engineered to create designer probiotics. Such innovative approaches include; a receptor mimicry strategy to create probiotics that target specific pathogens and toxins, a patho-biotechnology approach using pathogen-derived genes to create more robust probiotic stains with increased host and processing-associated stress tolerance profiles and meta-biotechnology, whereby, functional metagenomics may be used to identify novel genes from diverse and vastly unexplored environments, such as the human gut, for use in biotechnology and medicine.

What genomic sequence information has revealed about Vibrio ecology in the ocean--a review

To date, the genomes of eight Vibrio strains representing six species and three human pathogens have been fully sequenced and reported. This review compares genomic information revealed from these sequencing efforts and what we can infer about Vibrio biology and ecology from this and related genomic information. The focus of the review is on those attributes that allow the Vibrios to survive and even proliferate in their ocean habitats, which include seawater, plankton, invertebrates, fish, marine mammals, plants, man-made structures (surfaces), and particulate matter. Areas covered include general information about the eight genomes, each of which is distributed over two chromosomes; a discussion of expected and unusual genes found; attachment sites and mechanisms; utilization of particulate and dissolved organic matter; and conclusions.

Achievements and new knowledge unraveled by metagenomic approaches

Metagenomics has paved the way for cultivation-independent assessment and exploitation of microbial communities present in complex ecosystems. In recent years, significant progress has been made in this research area. A major breakthrough was the improvement and development of high-throughput next-generation sequencing technologies. The application of these technologies resulted in the generation of large datasets derived from various environments such as soil and ocean water. The analyses of these datasets opened a window into the enormous phylogenetic and metabolic diversity of microbial communities living in a variety of ecosystems. In this way, structure, functions, and interactions of microbial communities were elucidated. Metagenomics has proven to be a powerful tool for the recovery of novel biomolecules. In most cases, functional metagenomics comprising construction and screening of complex metagenomic DNA libraries has been applied to isolate new enzymes and drugs of industrial importance. For this purpose, several novel and improved screening strategies that allow efficient screening of large collections of clones harboring metagenomes have been introduced.

Evidence of methanesulfonate utilizers in the Sargasso Sea metagenome

Methanesulfonate (MSA) is one of the products of the photo-oxidation of dimethylsulfide in the atmosphere. The genes responsible for the import of MSA into the cell (msm EFGH) and for its oxidation to formaldehyde (msm ABCD) have been previously sequenced from the soil bacterium Methylosulfonomonas methylovora str. M2 while genes for an MSA monooxygenase have been sequenced from marine bacterium Marinosulfonomonas methylotropha str. TR3. We performed a sequence-based screening of the Sargasso Sea metagenome for homologues of the MSA monooxygenase (MSAMO) and MSA import genes. Our search retrieved one scaffold bearing genes with high identity to the msm ABCD cluster plus two scaffolds bearing genes highly identical to the msm EFGH operon. We increased the available data by sequencing two metagenome plasmids, which revealed more msm genes. In these three cases synteny with the original msm operons was revealed. We also retrieved several singletons showing high identity to shorter segments of the msm clusters or individual msm genes. Furthermore, a characteristic 26-aa internal spacer of the MsmA Rieske-type motif was conserved. Our findings support the case for a significant role of MSA degraders in the marine sulfur cycle and seem to suggest that they may be prominent members of the methylotrophic community in surface ocean waters.

Analysis of the Pseudoalteromonas tunicata genome reveals properties of a surface-associated life style in the marine environment

BACKGROUND

Colonisation of sessile eukaryotic host surfaces (e.g. invertebrates and seaweeds) by bacteria is common in the marine environment and is expected to create significant inter-species competition and other interactions. The bacterium Pseudoalteromonas tunicata is a successful competitor on marine surfaces owing primarily to its ability to produce a number of inhibitory molecules. As such P. tunicata has become a model organism for the studies into processes of surface colonisation and eukaryotic host-bacteria interactions.

METHODOLOGY/PRINCIPAL FINDINGS

To gain a broader understanding into the adaptation to a surface-associated life-style, we have sequenced and analysed the genome of P. tunicata and compared it to the genomes of closely related strains. We found that the P. tunicata genome contains several genes and gene clusters that are involved in the production of inhibitory compounds against surface competitors and secondary colonisers. Features of P. tunicata's oxidative stress response, iron scavenging and nutrient acquisition show that the organism is well adapted to high-density communities on surfaces. Variation of the P. tunicata genome is suggested by several landmarks of genetic rearrangements and mobile genetic elements (e.g. transposons, CRISPRs, phage). Surface attachment is likely to be mediated by curli, novel pili, a number of extracellular polymers and potentially other unexpected cell surface proteins. The P. tunicata genome also shows a utilisation pattern of extracellular polymers that would avoid a degradation of its recognised hosts, while potentially causing detrimental effects on other host types. In addition, the prevalence of recognised virulence genes suggests that P. tunicata has the potential for pathogenic interactions.

CONCLUSIONS/SIGNIFICANCE

The genome analysis has revealed several physiological features that would provide P. tunciata with competitive advantage against other members of the surface-associated community. We have also identified properties that could mediate interactions with surfaces other than its currently recognised hosts. This together with the detection of known virulence genes leads to the hypothesis that P. tunicata maintains a carefully regulated balance between beneficial and detrimental interactions with a range of host surfaces.

Selenate-dependent anaerobic arsenite oxidation by a bacterium from Mono Lake, California

Arsenate was produced when anoxic Mono Lake water samples were amended with arsenite and either selenate or nitrate. Arsenite oxidation did not occur in killed control samples or live samples with no added terminal electron acceptor. Potential rates of anaerobic arsenite oxidation with selenate were comparable to those with nitrate ( approximately 12 to 15 mumol.liter(-1) h(-1)). A pure culture capable of selenate-dependent anaerobic arsenite oxidation (strain ML-SRAO) was isolated from Mono Lake water into a defined salts medium with selenate, arsenite, and yeast extract. This strain does not grow chemoautotrophically, but it catalyzes the oxidation of arsenite during growth on an organic carbon source with selenate. No arsenate was produced in pure cultures amended with arsenite and nitrate or oxygen, indicating that the process is selenate dependent. Experiments with washed cells in mineral medium demonstrated that the oxidation of arsenite is tightly coupled to the reduction of selenate. Strain ML-SRAO grows optimally on lactate with selenate or arsenate as the electron acceptor. The amino acid sequences deduced from the respiratory arsenate reductase gene (arrA) from strain ML-SRAO are highly similar (89 to 94%) to those from two previously isolated Mono Lake arsenate reducers. The 16S rRNA gene sequence of strain ML-SRAO places it within the Bacillus RNA group 6 of gram-positive bacteria having low G+C content.

Diversity and abundance of glycosyl hydrolase family 5 in the North Atlantic Ocean

The diversity and abundance of glycosyl hydrolase family 5 (GH5) were studied in the North Atlantic Ocean. This family was chosen because of the large number of available sequences from cultured bacteria, the variety of substrates it targets, and the high number of similar sequences in the Sargasso Sea environmental genome database. Three clone libraries of a GH5 subcluster were constructed from the Mid-Atlantic Bight and the eastern and western North Atlantic Ocean. The two North Atlantic Ocean libraries did not differ from each other but both were significantly less diverse than the Mid-Atlantic Bight library. The abundance of GH5 genes estimated by quantitative PCR was positively correlated with chlorophyll concentrations in the eastern part of a transect from Fort Pierce, Florida, to the Azores and in a depth profile, suggesting that the supply of labile organic material selects for GH5-bearing bacteria in these waters. However, the data suggest that only <1% of all bacteria harbor the GH5 subcluster. These and other data suggest that the hydrolysis of polysaccharides requires complicated multi-enzyme systems.

A new role for sulfur in arsenic cycling

Sulfur and arsenic often coexist in the environment and share similar microbial redox transformations. We examined the effects of sulfide on aerobic arsenite oxidation in alkaline lake water samples and in laboratory enrichment cultures. Significant arsenite oxidation occurred only in treatments with bacteria present, and production of arsenate was greatly enhanced by the addition of sulfide or thiosulfate. IC-ICP-MS analysis of samples showed that mono- and dithioarsenate formed in arsenite + sulfide amended lake water. Our data indicate that these two thioarsenic compounds are fairly stable in sterile alkaline solutions, but are transformed predominantly to arsenate when bacteria are present. Enrichment culture experiments suggest that sulfur-oxidizing bacteria use free or arsenic-bound sulfur as a growth substrate and directly or indirectly transform arsenite and thioarsenates to arsenate during growth. Increases in cell density resulted in more rapid conversion of arsenite and thioarsenates. The rate and extent of these processes appearto be controlled bythe concentration of bacteria and the ratio of reduced sulfur to arsenite present. Sulfur-driven arsenite oxidation and microbial thioarsenate transformation may be important biogeochemical processes in the arsenic cycle of our study site (Mono Lake, CA, USA) and other alkaline environments as well.

Screening and purification for novel cytochrome b5 from uncultured environmental micro-organisms

AIMS

We describe a sequence-based PCR method suitable for the isolation of a novel soluble heme-binding domain of cytochrome b(5) (cyt b(5)) gene directly from metagenomic DNA is described.

METHODS AND RESULTS

Using the degenerate primer set, a cyt b(5) gene was isolated directly from metagenomic DNA. Based on the sequence-based PCR method, the similar conserved motif of cyt b(5) from Rhodopseudomonas palustris strain makes the novel target gene. The gene encoding cyt b(5) was cloned and expressed in Escherichia coli BL21 (DE3) using pET expression system. The expressed recombinant enzyme was purified by Ni-nitrilotriacetic acid affinity chromatography and characterized.

CONCLUSIONS

Sequence-based strategy is an effective method for application of the novel gene from metagenomic DNA.

SIGNIFICANCE AND IMPACT OF THE STUDY

Investigation of novel genes from metagenome, most of the micro-organism species are largely untapped, could represent an interesting and useful reservoir for biological processes.

Conservation of the chitin utilization pathway in the Vibrionaceae

Vibrionaceae are regarded as important marine chitin degraders, and attachment to chitin regulates important biological functions; yet, the degree of chitin pathway conservation in Vibrionaceae is unknown. Here, a core chitin degradation pathway is proposed based on comparison of 19 Vibrio and Photobacterium genomes with a detailed metabolic map assembled for V. cholerae from published biochemical, genomic, and transcriptomic results. Further, to assess whether chitin degradation is a conserved property of Vibrionaceae, a set of 54 strains from 32 taxa were tested for the ability to grow on various forms of chitin. All strains grew on N-acetylglucosamine (GlcNAc), the monomer of chitin. The majority of isolates grew on alpha (crab shell) and beta (squid pen) chitin and contained chitinase A (chiA) genes. chiA sequencing and phylogenetic analysis suggest that this gene is a good indicator of chitin metabolism but appears subject to horizontal gene transfer and duplication. Overall, chitin metabolism appears to be a core function of Vibrionaceae, but individual pathway components exhibit dynamic evolutionary histories.

Comparison of chitinolytic enzymes from an alkaline, hypersaline lake and an estuary

We examined the genetic and physiological characteristics of chitin degrading enzymes expressed by fosmids cloned from two strains of chitinolytic gammaproteobacteria isolated from alkaline, hypersaline Mono Lake, California; and from a metagenomic library derived from an estuarine bacterial community (Dean Creek, Sapelo Island, GA, USA). The Mono Lake chitinolytic enzymes presented unique adaptations in terms of halo- and alkalitolerance. The sequence from one of the Mono Lake isolates (strain 12A) was a conventional family 18 glycosyl hydrolase; however, the expressed protein had a novel secondary activity peak at pH 10. We obtained a novel family 20 glycosyl hydrolase sequence from Mono Lake strain AI21. The activity of the expressed protein had a pH optimum of 10, several pH units higher than any other enzyme currently assigned to this family, and the enzyme retained 80% of its activity at pH 11. The enzyme was also halotolerant, retaining activity in salt solutions of up to 225 g l(-1). Sequence analysis indicated a molecular weight of approximately 90 kDa for the protein, and that it contained two active sites. Culture supernatant contained two chitinolytic proteins, 45 and 31 kDa, suggesting possible post-expression modification of the gene product. In contrast, the sequence found in the estuarine metagenomic library and the functional characteristics of the protein expressed from it were those of a conventional family 18 glycosyl hydrolase.

Chitinase gene diversity at a deep sea station of the east Pacific nodule province

The Pacific nodule province covered about 4.5 million km(2) in the east tropical Pacific with an abundance of polymetallic nodules at the seafloor. In view of the environmental protection and resource preservation, the survey of biodiversity was important during the reconnaissance and exploitation in this area. As one of the important component of the deep sea ecosystem, the microbial community in the Pacific nodule province was still largely unknown. The chitinolytic bacteria diversity in deep-sea sediment of a station within the Pacific nodule province was examined by molecular technology. A total of 18 chitinase genes were detected by a set of degenerate PCR primer specific for chiA gene fragment of family 18 chitinase. Most of them belonged to the Serratia-like chitinase. Eight genes had different amino acid sequences in the conserved motif, encompassing the catalytic site among the ChiA protein of family 18 glycosyl hydrolases, and clustered in an independent clade on the phylygenetic tree.

Sulfide oxidation coupled to arsenate reduction by a diverse microbial community in a soda lake

We characterized the arsenate-reducing, sulfide-oxidizing population of Mono Lake, California, by analyzing the distribution and diversity of rrnA, cbbL, and dissimilatory arsenate reductase (arrA) genes in environmental DNA, arsenate-plus sulfide-amended lake water, mixed cultures, and isolates. The arsenate-reducing community was diverse. An organism represented by an rrnA sequence previously retrieved from Mono Lake and affiliated with the Desulfobulbaceae (Deltaproteobacteria) appears to be an important member of the arsenate-reducing, sulfide-oxidizing community. Sulfide oxidation coupled with arsenate reduction appears to proceed via a two-electron transfer, resulting in the production of arsenite and an intermediate S compound that is subsequently disproportionated. A realgar-like As/S mineral was formed in some experiments.

Metagenomics: DNA sequencing of environmental samples

Although genomics has classically focused on pure, easy-to-obtain samples, such as microbes that grow readily in culture or large animals and plants, these organisms represent only a fraction of the living or once-living organisms of interest. Many species are difficult to study in isolation because they fail to grow in laboratory culture, depend on other organisms for critical processes, or have become extinct. Methods that are based on DNA sequencing circumvent these obstacles, as DNA can be isolated directly from living or dead cells in various contexts. Such methods have led to the emergence of a new field, which is referred to as metagenomics.

Analysis of microbial gene transcripts in environmental samples

We analyzed gene expression in marine and freshwater bacterioplankton communities by the direct retrieval and analysis of microbial transcripts. Environmental mRNA, obtained from total RNA by subtractive hybridization of rRNA, was reverse transcribed, amplified with random primers, and cloned. Approximately 400 clones were analyzed, of which approximately 80% were unambiguously mRNA derived. mRNAs appeared to be from diverse taxonomic groups, including both Bacteria (mainly alpha- and gamma-Proteobacteria) and Archaea (mainly Euryarchaeota). Many transcripts could be linked to environmentally important processes such as sulfur oxidation (soxA), assimilation of C1 compounds (fdh1B), and acquisition of nitrogen via polyamine degradation (aphA). Environmental transcriptomics is a means of exploring functional gene expression within natural microbial communities without bias toward known sequences, and provides a new approach for obtaining community-specific variants of key functional genes.