Biogeographic and Quantitative Analyses of Abundant Uncultivated γ-Proteobacterial Clades from Marine Sediment

Bowman, John P.; McCammon, Sharee A.; Dann, Alison L.

doi:10.1007/s00248-004-0070-2

Cited by 35 publications

(22 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…One remarkable characteristic of the Pseudoalteromonas genus is that it can be divided in two major clades, including the pigmented strains, with a greater bioactivity, and non-pigmented strains, which tend to have more unusual enzymatic activities [24, 25, 28]. Notably, in the reported phylogeny there is a clear distinction between pigmented and non-pigmented strains: i) the pigmented clade displays a phylogeny with a greater degree of variability, embedding most of the species included in the dataset; ii) the non-pigmented clade is characterized by a phylogenetic shallowness, consistently with the literature and, since it mostly embeds strains from the P. haloplanktis species (as well as strains of the P. undina , P. marina, P. arctica species and still unassigned strains), it will be referred to as P. haloplanktis group ( P. h. -group).…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights

et al. 2017

View full text Add to dashboard Cite

Background Pseudoalteromonas is a genus of ubiquitous marine bacteria used as model organisms to study the biological mechanisms involved in the adaptation to cold conditions. A remarkable feature shared by these bacteria is their ability to produce secondary metabolites with a strong antimicrobial and antitumor activity. Despite their biotechnological relevance, representatives of this genus are still lacking (with few exceptions) an extensive genomic characterization, including features involved in the evolution of secondary metabolites production. Indeed, biotechnological applications would greatly benefit from such analysis.ResultsHere, we analyzed the genomes of 38 strains belonging to different Pseudoalteromonas species and isolated from diverse ecological niches, including extreme ones (i.e. Antarctica). These sequences were used to reconstruct the largest Pseudoalteromonas pangenome computed so far, including also the two main groups of Pseudoalteromonas strains (pigmented and not pigmented strains). The downstream analyses were conducted to describe the genomic diversity, both at genus and group levels. This allowed highlighting a remarkable genomic heterogeneity, even for closely related strains. We drafted all the main evolutionary steps that led to the current structure and gene content of Pseudoalteromonas representatives. These, most likely, included an extensive genome reduction and a strong contribution of Horizontal Gene Transfer (HGT), which affected biotechnologically relevant gene sets and occurred in a strain-specific fashion. Furthermore, this study also identified the genomic determinants related to some of the most interesting features of the Pseudoalteromonas representatives, such as the production of secondary metabolites, the adaptation to cold temperatures and the resistance to abiotic compounds.ConclusionsThis study poses the bases for a comprehensive understanding of the evolutionary trajectories followed in time by this peculiar bacterial genus and for a focused exploitation of their biotechnological potential.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3382-y) contains supplementary material, which is available to authorized users.

show abstract

Section: Resultsmentioning

confidence: 99%

“…Some Pseudoalteromonas representatives are well known for their ability to antagonize the growth of bacteria, algae, fungi and parasites [24, 25, 28, 47], suggesting the presence of genes involved in the biosynthesis of antimicrobial compounds. These genes have been searched in the Pseudoalteromonas genomes.…”

Section: Resultsmentioning

confidence: 99%

The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights

et al. 2017

View full text Add to dashboard Cite

show abstract

“…The only two nontarget sequences retrieved from Alphaproteobacteria DGGE (bands 6A‐S1 and 7A‐S3) were affiliated to Ectothiorhodospiraceae . Members of this family are involved in sulphur oxidation processes and were reported to be highly abundant in surface marine sediments (Bowman et al , 2005). A high abundance of Ectothiorhodospiraceae populations in mangrove sediments may have favored its unspecific amplification.…”

Section: Discussionmentioning

confidence: 99%

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

Gomes¹,

Borges²,

Paranhos³

et al. 2008

FEMS Microbiology Ecology

129

View full text Add to dashboard Cite

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.

show abstract

“…Another important limitation in the interpretation of diversity data from human‐impacted environments is our incomplete knowledge of the biogeography of marine microorganisms and the relevant environmental factors determining their distribution. In recent years, there have been some efforts aiming to explain the distribution of marine bacterioplankton and sediment microorganisms (Bowman et al , 2005; Pommier et al , 2007; Fuhrman, 2009). This background knowledge is very important for the interpretation of data from human‐impacted environments.…”

Section: Methodsological Aspects For the Assessment Of Anthropogenic Ementioning

confidence: 99%

Anthropogenic perturbations in marine microbial communities

et al. 2011

View full text Add to dashboard Cite

Human activities impact marine ecosystems at a global scale and all levels of complexity of life. Despite their importance as key players in ecosystem processes, the stress caused to microorganisms has been greatly neglected. This fact is aggravated by difficulties in the analysis of microbial communities and their high diversity, making the definition of patterns difficult. In this review, we discuss the effects of nutrient increase, pollution by organic chemicals and heavy metals and the introduction of antibiotics and pathogens into the environment. Microbial communities respond positively to nutrients and chemical pollution by increasing cell numbers. There are also significant changes in community composition, increases in diversity and high temporal variability. These changes, which evidence the modification of the environmental conditions due to anthropogenic stress, usually alter community functionality, although this aspect has not been explored in depth. Altered microbial communities in human-impacted marine environments can in turn have detrimental effects on human health (i.e. spread of pathogens and antibiotic resistance). New threats to marine ecosystems, i.e. related to climate change, could also have an impact on microbial communities. Therefore, an effort dedicated to analyse the microbial compartment in detail should be made when studying the impact of anthropogenic activities on marine ecosystems.

show abstract

Biogeographic and Quantitative Analyses of Abundant Uncultivated γ-Proteobacterial Clades from Marine Sediment

Cited by 35 publications

References 30 publications

The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights

The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights

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

Anthropogenic perturbations in marine microbial communities

Contact Info

Product

Resources

About