Diversity of Bacteria in the Marine Sponge Aplysina fulva in Brazilian Coastal Waters

Hardoim, Cristiane Cassiolato Pires; Costa, Rodrigo; Araújo, Fábio Vieira de; Hajdu, Eduardo; Peixoto, Raquel S.; Lins, Ulysses; Rosado, Alexandre Soares; Elsas, Jan Dirk van

doi:10.1128/aem.05552-11

Cited by 25 publications

(35 citation statements)

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“…Comparison with previous studies on spongeassociated microbial communities Before the establishment of pyrosequencing technology, molecular techniques with lower resolution have recovered up to 20 bacterial phyla and both major archaeal lineages, Crenarchaeota and Euryarchaeota, from sponges (Taylor et al, 2007;Hardoim et al, 2009). The number of bacterial phyla reported in sponges was increased to 26 with the addition of Fusobacteria, Tenericutes, Deferribacteres, Fibrobacteres, BRC1 and WS3 by a study using tag pyrosequencing (Webster et al, 2009).…”

Section: Influence Of Environment On Microbial Communitiesmentioning

confidence: 99%

Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea

et al. 2010

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Marine sponges are associated with a remarkable array of microorganisms. Using a tag pyrosequencing technology, this study was the first to investigate in depth the microbial communities associated with three Red Sea sponges, Hyrtios erectus, Stylissa carteri and Xestospongia testudinaria. We revealed highly diverse sponge-associated bacterial communities with up to 1000 microbial operational taxonomic units (OTUs) and richness estimates of up to 2000 species. Altogether, 26 bacterial phyla were detected from the Red Sea sponges, 11 of which were absent from the surrounding sea water and 4 were recorded in sponges for the first time. Up to 100 OTUs with richness estimates of up to 300 archaeal species were revealed from a single sponge species. This is by far the highest archaeal diversity ever recorded for sponges. A non-negligible proportion of unclassified reads was observed in sponges. Our results demonstrated that the sponge-associated microbial communities remained highly consistent in the same sponge species from different locations, although they varied at different degrees among different sponge species. A significant proportion of the tag sequences from the sponges could be assigned to one of the sponge-specific clusters previously defined. In addition, the sponge-associated microbial communities were consistently divergent from those present in the surrounding sea water. Our results suggest that the Red Sea sponges possess highly sponge-specific or even sponge-species-specific microbial communities that are resistant to environmental disturbance, and much of their microbial diversity remains to be explored.

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Section: Influence Of Environment On Microbial Communitiesmentioning

confidence: 99%

Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea

et al. 2010

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“…The DGGE profiles were analyzed using GelCompar II software (version 4.06; Applied Maths, Kortrijk, Belgium). The Pearson correlation coefficient was calculated on the basis of the densitometric curves of the profile lanes as described previously (28). Dendrograms were constructed through a Ward-based coefficient using BioNumerics software (Applied Maths).…”

Section: Methodsmentioning

confidence: 99%

Bacterial Community Response to Petroleum Hydrocarbon Amendments in Freshwater, Marine, and Hypersaline Water-Containing Microcosms

Jurelevicius

Alvarez

Marques

et al. 2013

Appl Environ Microbiol

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Hydrocarbon-degrading bacterial communities from freshwater, marine, and hypersaline Brazilian aquatic ecosystems (with water salinities corresponding to 0.2%, 4%, and 5%, respectively) were enriched with different hydrocarbons (heptadecane, naphthalene, or crude oil). Changes within the different microcosms of bacterial communities were analyzed using cultivation approaches and molecular methods (DNA and RNA extraction, followed by genetic fingerprinting and analyses of clone libraries based on the 16S rRNA-coding gene). A redundancy analysis (RDA) of the genetic fingerprint data and a principal component analysis (PCA) of the clone libraries revealed hydrocarbon-enriched bacterial communities specific for each ecosystem studied. However, within the same ecosystem, different bacterial communities were selected according to the petroleum hydrocarbon used. In general, the results demonstrated that Acinetobacter and Cloacibacterium were the dominant genera in freshwater microcosms; the Oceanospirillales order and the Marinobacter, Pseudomonas, and Cycloclasticus genera predominated in marine microcosms; and the Oceanospirillales order and the Marinobacter genus were selected in the different hydrocarbon-containing microcosms in hypersaline water. Determination of total petroleum hydrocarbons (TPHs) in all microcosms after 32 days of incubation showed a decrease in the hydrocarbon concentration compared to that for the controls. A total of 50 (41.3%) isolates from the different hydrocarbon-contaminated microcosms were associated with the dominant operational taxonomic units (OTUs) obtained from the clone libraries, and their growth in the hydrocarbon contaminating the microcosm from which they were isolated as the sole carbon source was observed. These data provide insight into the general response of bacterial communities from freshwater, marine, and hypersaline aquatic ecosystems to petroleum hydrocarbon contamination.

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“…For example, the candidate phylum TM7 has been found repeatedly in many different environments. A sequence corresponding to the 16S rRNA gene of TM7 was first found in peat bogs (65), and it has since been reported to be present in a multitude of diverse environments, including soil, water, waste treatment sludge, marine sponges, the human microbiome, and many others (10,20,31,32). TM7 is just one broadly distributed phylum that has resisted substantial cultivation efforts; as indicated above, most bacterial taxa have never been studied in the lab, representing enormous genetic and biochemical diversity.…”

Section: How Do We Know There Are Unculturable Bacteria?mentioning

confidence: 99%

Growing Unculturable Bacteria

2012

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The bacteria that can be grown in the laboratory are only a small fraction of the total diversity that exists in nature. At all levels of bacterial phylogeny, uncultured clades that do not grow on standard media are playing critical roles in cycling carbon, nitrogen, and other elements, synthesizing novel natural products, and impacting the surrounding organisms and environment. While molecular techniques, such as metagenomic sequencing, can provide some information independent of our ability to culture these organisms, it is essentially impossible to learn new gene and pathway functions from pure sequence data. A true understanding of the physiology of these bacteria and their roles in ecology, host health, and natural product production requires their cultivation in the laboratory. Recent advances in growing these species include coculture with other bacteria, recreating the environment in the laboratory, and combining these approaches with microcultivation technology to increase throughput and access rare species. These studies are unraveling the molecular mechanisms of unculturability and are identifying growth factors that promote the growth of previously unculturable organisms. This minireview summarizes the recent discoveries in this area and discusses the potential future of the field. What is an unculturable bacterium? While at first glance, there appears to be a contradiction in the title of this review, in this context, "unculturable" indicates that current laboratory culturing techniques are unable to grow a given bacterium in the laboratory. That all organisms must be growing in their natural environment is axiomatic; that many we cannot currently grow will be cultured in the future is certain. Therefore, "unculturable" does not mean "can never be cultured" but, rather, signifies that we lack critical information on their biology, and this presents both challenges and opportunities. These opportunities are the chance to learn the molecular principles behind this recalcitrant growth, allowing us to add that information to our repertoire of microbiological techniques and gaining access to previously hidden metabolic diversity that will provide new natural products and reveal factors that can contribute to both ecological balance and host health. This review examines the recent approaches that microbiologists are employing to convert currently unculturable bacteria into cultured isolates in the laboratory while concurrently beginning to discover the mechanisms behind their apparent unculturability.

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Diversity of Bacteria in the Marine Sponge Aplysina fulva in Brazilian Coastal Waters

Cited by 25 publications

References 0 publications

Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea

Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea

Bacterial Community Response to Petroleum Hydrocarbon Amendments in Freshwater, Marine, and Hypersaline Water-Containing Microcosms

Growing Unculturable Bacteria

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