Improved culturability of SAR11 strains in dilution-to-extinction culturing from the East Sea, West Pacific Ocean

Song, Jaeho; Oh, Hyun-Myung; Cho, Jang-Cheon

doi:10.1111/j.1574-6968.2009.01623.x

Cited by 83 publications

(54 citation statements)

References 23 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…4b). In the class Alpha-proteobacteria, most clones of the samples of 1,000 m and 10 m belonged to the pelagic bacterial groups of the SAR clade that have been ubiquitously and predominantly detected in the East Sea (Song et al, 2009). As described, the back trajectory analysis showed that the air masses at 1,000 m and 10 m were suspended over the Sea of Japan in the 3 days prior to sampling.…”

Section: Bacterial Populations Carried From Marine Regionsmentioning

confidence: 97%

Vertical distribution of airborne bacterial communities in an Asian-dust downwind area, Noto Peninsula

Maki

Hara

Kobayashi

et al. 2015

Atmospheric Environment

View full text Add to dashboard Cite

Bioaerosols at high altitudes were collected using an aircraft and a balloon.Pyrosequencing using 16S rDNA revealed vertical distributions of airborne bacteria.16S rDNA clone libraries suggested the transport of terrestrial and marine bacteria.Meteorological conditions contribute to vertical variations in airborne bacteria. 3 AbstractBacterial populations transported from ground environments to the atmosphere get dispersed throughout downwind areas and can influence ecosystem dynamics, human health, and climate change. However, the vertical bacterial distribution in the free troposphere was rarely investigated in detail. We collected aerosols at altitudes of 3,000 m, 1,000 m, and 10 m over the Noto Peninsula, Japan, where the westerly winds carry aerosols from continental and marine areas. During the sampling period on March 10, 2012, the air mass at 3,000 m was transported from the Chinese desert region by the westerly winds, and a boundary layer was formed below 2,000 m. Pyrosequencing targeting 16S rRNA genes (16S rDNA) revealed that the bacterial community at 3,000 m was predominantly composed of terrestrial bacteria, such as Bacillus and Actinobacterium species. In contrast, those at 1,000 m and 10 m included marine bacteria belonging to the classes Cyanobacteria and Alphaproteobacteria. The entire 16S rDNA sequences in the clone libraries were identical to those of the terrestrial and marine bacterial species, which originated from the Chinese desert region and the Sea of Japan, respectively. The origins of air masses and meteorological conditions contribute to vertical variations in the bacterial communities in downwind atmosphere.

show abstract

Section: Bacterial Populations Carried From Marine Regionsmentioning

confidence: 97%

Vertical distribution of airborne bacterial communities in an Asian-dust downwind area, Noto Peninsula

Maki

Hara

Kobayashi

et al. 2015

Atmospheric Environment

View full text Add to dashboard Cite

show abstract

“…In addition, the role of proteorhodopsin is starting to become clear, which may lead to a better understanding of the carbon flux in the ocean (78). This culture technique has now led to the culture of new members of this clade from different marine regions (75) as well as other previously uncultured isolates from both marine and freshwater environments (15,33,36,59,79).…”

Section: Approaches To Culturing the Missing Bacterial Diversitymentioning

confidence: 99%

Growing Unculturable Bacteria

2012

View full text Add to dashboard Cite

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.

show abstract

“…(Eguchi et al, 1996) are known to be ubiquitous marine oligotrophic ultramicrobacteria, which are thought to demonstrate improved survival at low substrate concentrations. The SAR clade is composed of ubiquitous and unculturable marine bacteria detected in the Sea of Japan (Song et al, 2009) and in ocean areas such as the Pacific Ocean (Giovannoni and Stingl 2005). Members of Pelagibacter, including the SAR clade, occupy approximately 25%-50% of marine bacteria in ocean areas, indicating their ability to survive in extreme environments (Morris et al, 2002).…”

Section: Alphaproteobacteriamentioning

confidence: 99%

Variations in the structure of airborne bacterial communities in a downwind area during an Asian dust (Kosa) event

Maki¹,

Puspitasari²,

Hara³

et al. 2014

Science of The Total Environment

View full text Add to dashboard Cite

Asian dust (Kosa) events transport airborne microorganisms that significantly impact biological ecosystems, human health, and ice-cloud formation in downwind areas.However, the composition and population dynamics of airborne bacteria have rarely been investigated in downwind areas during Kosa events. In this study, air samplings were sequentially performed at the top of a 10-m high building within the Kosa event arrival area (Kanazawa city, Japan) from May 1 to May 7, 2011, during a Kosa event.The particle concentrations of bacterial cells and mineral particles was ten-fold higher during the Kosa event than on non-Kosa event days. A 16S ribosomal DNA clone library prepared from the air samples primarily contained sequences from three phyla:Cyanobacteria, Firmicutes, and Alphaproteobacteria. The clones from Cyanobacteria were mainly from a marine type of Synechococcus species that was dominant during the first phase of the Kosa event and was continuously detected throughout the Kosa event.The clones from Alphaproteobacteria were mainly detected at the initial and final periods of the Kosa event, and phylogenetic analysis showed that their sequences clustered with those from a marine bacterial clade (the SAR clade) and Sphingomonas spp. During the middle of the Kosa event, the Firmicutes species Bacillus subtilis and Bacillus pumilus were predominant; these species are known to be predominat in the atmosphere above the Chinese desert, which is the source of the dust during Kosa events. The clones obtained after the Kosa event had finished were mainly from Bacillus megaterium, which is thought to originate from local terrestrial areas. Our results suggest that airborne bacterial communities at the ground level in areas affected 2 by Kosa events change their species compositions during a Kosa event toward those containing terrestrial and pelagic bacteria transported from the Sea of Japan and the continental area of China by the Kosa event.

show abstract

Improved culturability of SAR11 strains in dilution-to-extinction culturing from the East Sea, West Pacific Ocean

Cited by 83 publications

References 23 publications

Vertical distribution of airborne bacterial communities in an Asian-dust downwind area, Noto Peninsula

Vertical distribution of airborne bacterial communities in an Asian-dust downwind area, Noto Peninsula

Growing Unculturable Bacteria

Variations in the structure of airborne bacterial communities in a downwind area during an Asian dust (Kosa) event

Contact Info

Product

Resources

About