The breakthrough of environmental genomics of marine microbes has revealed the existence of eubacterial rhodopsin in the sea, named proteorhodopsin (PR), which can take light to produce bio-energy ...for cell metabolism. Gene and protein sequence analysis and laser flash-induced photolysis experiments have validated the function of PR as light-driven proton-pump. During the pumping process, light energy is transformed into chemical gradient potential across plasma inner-membrane, the potential energy is then used to synthesize ATR The finding of PR actually brings to light a novel pathway of sunlight utilization existing in heterotrophic eubacteria in contrast to the well-known chlorophyll-dependent photosynthesis in the sea. Since the group of PR-bearing bacteria is one of the numerically richest microorganisms on the Earth, accounting for 13% of the total in sea surface water, and with averaged cellular PR molecules of 2.5x10(4), PR-bearing bacteria are a key component not to be ignored in energy metabolism and carbon cycling in the sea. Based on the understanding of current literature and our own investigation on PR in the China seas which indicated a ubiquitous presence and high diversity of PR in all the marine environments, we propose a conceptual model of energy flow and carbon cycling driven by both pigment-dependent and -independent biological utilization of light in the ocean.
Unicellular marine cyanobacteria are abundant in both coastal and oligotrophic environments, where they contribute substantially to primary production. The physiological effect of future increases in ...atmospheric CO2 concentrations on the marine picocyanobacteria is still poorly known. We studied the physiological changes in marine phycocyanin (PC)-rich and phycoerythrin (PE)-rich Synechococcus strains under different CO2 partial pressures (350, 600 and 800 ppm). The PE strain showed no significant change in growth rate over the experimental CO2 range. A significant increase (25.4%) in carbohydrate was observed at 800 ppm CO2, but no significant change in protein and RNA/DNA ratio was observed in any CO2 treatment. The PC strain showed a significant increase (36.7%) in growth rate at 800 ppm CO2, but no significant change in carbohydrate or protein content was observed over the entire CO2 range. The RNA/DNA ratio increased with increasing CO2 concentration and was positively correlated with growth rate. Cellular red fluorescence and orange fluorescence of the PE strain tended to decline in all CO2 treatments. However, no such decline was observed at higher CO2 treatments in the PC strain. Our results suggest that the PC strain would probably benefit more than the PE strain from future increases in atmospheric CO2 concentrations.
NSFC 40632013, 40576063; MOST 2005AA635240; NKBRD 2007CB815904; CFKSTI 704029
Picoplankton biomass and community structure in the subtropical and subarctic Pacific Oceans were investigated during ...November 2003, April-August 2005 and July-August 2005. The sampling covered the subarctic K2 station, the Western North Pacific subtropical gyre (WNPG1 and 2 stations) and the Eastern North Pacific subtropical area (ENP1, 2, 3 and 4 stations). Distinct differences in community structure and autotrophic and heterotrophic picoplankton biomass were observed among the above provinces. In subtropical areas, the picoplankton community comprised Prochlorococcus, Synechococcus, picoeukaryotes and heterotrophic bacteria. While in the subarctic area (K2 station), Prochlorococcus were absent. Prochlorococcus were numerically dominant in the subtropical oceans, their abundance tended to decrease with increasing nutrient levels, which is the opposite of the other picoplankton populations. Although the aerobic anoxygenic phototrophic heterotrophic bacteria (AAPB). accounted for only a small proportion of total heterotrophic bacterial abundance, their potential contribution to carbon export may be important due to their larger cell size and higher cell turnover rates compared with other heterotrophic bacteria. Biomass contribution of the AAPB increased distinctly along the oligotrophic to relatively eutrophic gradient. Vertically, AAPB generally followed the phytoplankton except in the subtropical WNPG. Spatial variability of biomass in the autotrophic picoplankton was distinctly larger than that in the heterotrophic bacteria. Changes in the picoplankton community were more closely associated with latitude while nutrient availability was more important for differences in picoplankton biomass. The biomass of autotrophic picoplankton in the upper mixed layer, and also the depth attenuation, were higher in eutrophic relative to oligotrophic waters. Picoplankton seemed to be an important source of new organic carbon for higher trophic level organisms and for detritus production, especially in the oligotrophic subtropical gyre. (C) 2008 Elsevier Ltd. All rights reserved.
National Institutes of Health (NIH) U01-HG02712; NSFC 40906079; MOST 2007CB815904; Ph.D. Programs Foundation of Ministry of Education of China 200803841021
Background: Members of the Roseobacter ...clade which play a key role in the biogeochemical cycles of the ocean are diverse and abundant, comprising 10-25% of the bacterioplankton in most marine surface waters. The rapid accumulation of whole-genome sequence data for the Roseobacter clade allows us to obtain a clearer picture of its evolution. Methodology/Principal Findings: In this study about 1,200 likely orthologous protein families were identified from 17 Roseobacter bacteria genomes. Functional annotations for these genes are provided by iProClass. Phylogenetic trees were constructed for each gene using maximum likelihood (ML) and neighbor joining (NJ). Putative organismal phylogenetic trees were built with phylogenomic methods. These trees were compared and analyzed using principal coordinates analysis (PCoA), approximately unbiased (AU) and Shimodaira-Hasegawa (SH) tests. A core set of 694 genes with vertical descent signal that are resistant to horizontal gene transfer (HGT) is used to reconstruct a robust organismal phylogeny. In addition, we also discovered the most likely 109 HGT genes. The core set contains genes that encode ribosomal apparatus, ABC transporters and chaperones often found in the environmental metagenomic and metatranscriptomic data. These genes in the core set are spread out uniformly among the various functional classes and biological processes. Conclusions/Significance: Here we report a new multigene-derived phylogenetic tree of the Roseobacter clade. Of particular interest is the HGT of eleven genes involved in vitamin B12 synthesis as well as key enzynmes for dimethylsulfoniopropionate (DMSP) degradation. These aquired genes are essential for the growth of Roseobacters and their eukaryotic partners.
A Gram-negative, non-motile, short-rod-shaped bacterial strain (JLT1210(T)) that accumulates poly-beta-hydroxybutyrate granules was isolated from the Beibu Gulf in the South China Sea. Cells have ...polar or subpolar flagella. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain belongs to the genus Oceanicola in the order Rhodobacterales, class Alphaproteobacteria. The closest neighbours were Oceanicola nanhaiensis SS011B1-20(T) (96.5 % similarity) and Oceanicola batsensis HTCC2597(T) (96.4 %). The predominant respiratory ubiquinone of strain JLT1210(T) was Q-10 and the DNA G+C content was 72.8 mol%. Evidence from genotypic, chemotaxonomic and phenotypic data shows that strain JLT1210(T) represents a novel species of the genus Oceanicola, for which the name Ocean/cola nitratireducens sp. nov. is proposed; the type strain is JLT1210(T) (=LMG 24663(T)=CGMCC 1.7292(T)).
MOST 2007CB815900; NSFC 40632013; SOA 200805068; National Infrastructure of Natural Resources for Science and Technology Program of China 2005DKA21209; COMRA DYXM-115-02-4-3; Technical Innovation Project of Ministry of Education of China 704029
A Gram-negative, non-motile, short-rod-shaped bacterial strain (JLT1210(T)) that accumulates poly-beta-hydroxybutyrate granules was isolated from the Beibu Gulf in the South China Sea. Cells have ...polar or subpolar flagella. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain belongs to the genus Oceanicola in the order Rhodobacterales, class Alphaproteobacteria. The closest neighbours were Oceanicola nanhaiensis SS011B1-20(T) (96.5 % similarity) and Oceanicola batsensis HTCC2597(T) (96.4 %). The predominant respiratory ubiquinone of strain JLT1210(T) was Q-10 and the DNA G+C content was 72.8 mol%. Evidence from genotypic, chemotaxonomic and phenotypic data shows that strain JLT1210(T) represents a novel species of the genus Oceanicola, for which the name Ocean/cola nitratireducens sp. nov. is proposed; the type strain is JLT1210(T) (=LMG 24663(T)=CGMCC 1.7292(T)).
MOST 2007CB815900; NSFC 40632013; SOA 200805068; National Infrastructure of Natural Resources for Science and Technology Program of China 2005DKA21209; COMRA DYXM-115-02-4-3; Technical Innovation Project of Ministry of Education of China 704029
NSFC 40632013; MOST 2007CB815904, 2006BAC11B04; COMRA DYXM-115-02-4-3; SOA 2008418068
Proteorhodopsin (PR) genes related to Flavobacteria were found to be highly diverse in the East and South China ...seas and displayed a distinct geographic pattern, which appeared to reflect cold versus warm adaptation when Global Oceanic Sampling database metagenomic data were included. Flavobacterial PR genes were more abundant offshore than nearshore, implying that inheritance of the PR gene could be important for Flavobacteria living in the oligotrophic environment.
NSFC 40632013, 40521003; MOST 200805068, 2006BAC11B04
In order to explore the responses of the bacterioplankton community to different types of aquaculture environments, three mariculture ponds ...comprised of groupers (Epinephelus diacanthus, ED), prawns (Penaeus vannamei, PV), and abalone (Haliotis diversicolor supertexta, HDS) in southeast, coastal China were investigated. The free-living bacterial diversity was analyzed through the construction of 16S rDNA clone library. A total of 203 16S rDNA sequences from three clone libraries were classified into 118 operational taxonomic units (OTUs), of which 51, 31, and 42 OTUs were distributed in the ED, PV, and HDS pond, respectively, with Bacteroidetes (30.6%), Actinobacteria (55.2%), and Cyanobacteria (32.8%) as the dominant division in the respective ponds. Meanwhile, each pond occupied some unique OTUs that were affiliated with uncommon (sub-) phyla, such as candidate OP11 division, Acidobacteria, Deltaproteobacteria, Planctomycetes, and Verrucomicrobia. Bacterial diversity in the ED pond was the richest, followed by the HDS and the PV pond. OTUs of 61.9% and 94.9% have less than 90% and 97% similarity to their nearest neighbors in public databases, respectively. All OTUs were grouped into 67 clusters, covering 11 (sub-) phyla. The OTUs only from single pond distributed in 53 clusters (79.1%), the OTUs shared by two ponds were affiliated with 14 clusters (20.9%), and none of clusters was formed by the OTUs which commonly originated from the three pond libraries, suggesting that the composition of bacterial populations in these ponds were significantly different. These results indicate that the aquatic environment created by different mariculture animals may foster very special and complex bacterial communities.
NSFC 40632013, 40521003; MOST 200805068, 2006BAC11B04
In order to explore the responses of the bacterioplankton community to different types of aquaculture environments, three mariculture ponds ...comprised of groupers (Epinephelus diacanthus, ED), prawns (Penaeus vannamei, PV), and abalone (Haliotis diversicolor supertexta, HDS) in southeast, coastal China were investigated. The free-living bacterial diversity was analyzed through the construction of 16S rDNA clone library. A total of 203 16S rDNA sequences from three clone libraries were classified into 118 operational taxonomic units (OTUs), of which 51, 31, and 42 OTUs were distributed in the ED, PV, and HDS pond, respectively, with Bacteroidetes (30.6%), Actinobacteria (55.2%), and Cyanobacteria (32.8%) as the dominant division in the respective ponds. Meanwhile, each pond occupied some unique OTUs that were affiliated with uncommon (sub-) phyla, such as candidate OP11 division, Acidobacteria, Deltaproteobacteria, Planctomycetes, and Verrucomicrobia. Bacterial diversity in the ED pond was the richest, followed by the HDS and the PV pond. OTUs of 61.9% and 94.9% have less than 90% and 97% similarity to their nearest neighbors in public databases, respectively. All OTUs were grouped into 67 clusters, covering 11 (sub-) phyla. The OTUs only from single pond distributed in 53 clusters (79.1%), the OTUs shared by two ponds were affiliated with 14 clusters (20.9%), and none of clusters was formed by the OTUs which commonly originated from the three pond libraries, suggesting that the composition of bacterial populations in these ponds were significantly different. These results indicate that the aquatic environment created by different mariculture animals may foster very special and complex bacterial communities.
P>1. Community structures of planktonic ammonia-oxidising archaea (AOA) and bacteria (AOB) were investigated for five high-altitude Tibetan lakes, which could be classified as freshwater, oligosaline ...or mesosaline, to develop a general view of the AOA and AOB in lakes on the Tibetan Plateau. 2. Based on PCR screening of the ammonia monooxygenase alpha-subunit (amoA) gene, AOA were present in 14 out of 17 samples, whereas AOB were detected in only four samples. Phylogenetic analyses indicated that the AOB communities were dominated by a unique monophylogenetic lineage within Nitrosomonas, which may represent a novel cluster of AOB. AOA, on the other hand, were distinct among lakes with different salinities. 3. Multivariate statistical analyses indicated a heterogeneous distribution of the AOA communities among lakes largely caused by lake salinity, whereas the uniform chemical properties within lakes and their geographical isolation may favour relatively homogeneous AOA communities within lakes. 4. Our results suggest a wide occurrence of AOA in Tibetan lakes and provide the first evidence of salinity-related differentiation of AOA community composition as well as potential geographical isolation of AOA in inland aquatic environments.
MOST 2007CB815904, 2005CB422004; NSFC 40632013, 40871045; SOA 200805068
