<i>Proteobacteria</i> and <i>Bacteroidetes</i> are major phyla of filterable bacteria passing through 0.22 μm pore size membrane filter, in Lake Sanaru, Hamamatsu, Japan

Maejima, Yoshiaki; Kushimoto, Koya; Muraguchi, Yusuke; Fukuda, Kohei; Miura, Takamasa; Yamazoe, Atsushi; Kimbara, Kazuhide; Shintani, Masaki

doi:10.1080/09168451.2018.1456317

Cited by 19 publications

(11 citation statements)

References 22 publications

(28 reference statements)

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“…The 16S rRNA gene-containing fragment of approximately 1.5 kb was amplified with the 27F ( ) and 1492R ( ) primers using 2 μl DNA as the template, and the PCR products were sequenced [ 20 ]. PCR was done with a total volume of 50 μl, which contained 27.8 μl Sterilized H 2 O, 5 μl 10×PCR Buffer, 5 μl dNTP Mix, 4μl MgCl 2 , 3 μl Primer1, 3 μl Primer2, 0.2 μl Taq DNA Polymerase and 2 μl Template DNA.…”

Section: Methodsmentioning

confidence: 99%

Isolation and characterization marine bacteria capable of degrading lignin-derived compounds

Wang

Zhang

et al. 2020

PLoS ONE

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Lignin, a characteristic component of terrestrial plants. Rivers transport large amounts of vascular plant organic matter into the oceans where lignin can degrade over time; however, microorganisms involved in this degradation have not been identified. In this study, several bacterial strains were isolated from marine samples using the lignin-derived compound vanillic acid (4-hydroxy-3-methoxybenzoic acid) as the sole carbon and energy source. The optimum growth temperature for all isolates ranged from 30 to 35˚C. All isolates grew well in a wide NaCl concentration range of 0 to over 50 g/L, with an optimum concentration of 22.8 g/L, which is the same as natural seawater. Phylogenetic analysis indicates that these strains are the members of Halomonas, Arthrobacter, Pseudoalteromonas, Marinomonas, and Thalassospira. These isolates are also able to use other lignin-derived compounds, such as 4-hydroxybenzoic acid, ferulic acid, syringic acid, and benzoic acid. Vanillic acid was detected in all culture media when isolates were grown on ferulic acid as the sole carbon source; however, no 4-hydroxy-3-methoxystyrene was detected, indicating that ferulic acid metabolism by these strains occurs via the elimination of two side chain carbons. Furthermore, the isolates exhibit 3,4-dioxygenase or 4,5-dioxygenase activity for protocatechuic acid ring-cleavage, which is consistent with the genetic sequences of related genera. This study was conducted to isolate and characterize marine bacteria of degrading ligninderived compounds, thereby revealing the degradation of aromatic compounds in the marine environment and opening up new avenues for the development and utilization of marine biological resources.

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Section: Methodsmentioning

confidence: 99%

Isolation and characterization marine bacteria capable of degrading lignin-derived compounds

Wang

Zhang

et al. 2020

PLoS ONE

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“…To investigate the abundance and community structure of bacteria, water samples are typically filtered using 0.2-0.45-µm pore-size filters, because most bacterial cells are trapped on filters with pores of this size; however, microbes in 0.2-µm filtrate have been reported from aquatic environments (e.g., MacDonell & Hood 1982, Hahn et al 2003, Miteva & Brenchley 2005, Maejima et al 2018). As 0.2-µm-filterable microbes, two types of ultrasmall cells have been reported (Torrella & Morita 1981, Duda et al 2012: ones that have a larger cell size when incubated with adequate nutrients (Torrella & Morita 1981, Hahn 2004, and others that are ultrasmall cells (obligate ultramicrobacteria) even when incubated with nutrient-rich media (Torrella & Morita 1981, Schut et al 1997, Rappé et al 2002, Hahn et al 2003, Nakai et al 2016.…”

Section: Introductionmentioning

confidence: 99%

High growth potential of transiently 0.2-µm-filterable bacteria with extracellular protease activity in coastal seawater

Obayashi

2019

Plankton Benthos Res

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Bacteria that pass through a 0.2-µm pore-size filter (0.2-µm-filterable bacteria) have been reported from various aquatic environments. It has been recognized that some 0.2-µm-filterable bacteria are transiently small/thin cells, which are considered as starvation forms of heterotrophic bacteria, especially in oligotrophic environments. However, whether these transiently 0.2-μm-filterable bacteria have roles in organic matter processing in aquatic environments has not yet been well described. Here we found high potential of the transiently 0.2-µm-filterable bacteria with extracellular protease activity in their natural nutritional condition. We conducted microcosm experiments using 0.2-µm-filtered coastal seawater (FSW) without any nutritional amendment, and monitored changes of the cell numbers trapped on a 0.2-µm filter (not 0.2-µm-filterable cells anymore) and their community structure in the FSW microcosms, with extracellular protease activities as indicators of heterotrophic microbial activity. We observed a rapid increase in the 0.2-µm-trapped cell number in the FSW microcosms that originally included only 0.2-µm-filterable microbes. The regenerating 0.2-µm-trapped cells were typical marine bacteria (Alphaproteobacteria, Gammaproteobacteria, Flavobacteriia). Extracellular aminopeptidase activities increased with increasing numbers of 0.2-µm-trapped cells. These results suggest that transiently 0.2-µm-filterable-form bacteria in the original coastal seawater recovered their size and were producing extracellular proteases, which might catalyze organic matter processing in seawater. Since organic nutrients were not added, the size increase might be caused by the reduction in competition from larger bacteria and/or the absence of grazing pressure. Our results demonstrate the growth potential and extracellular protease activity of transiently 0.2-μm-filterable bacteria in seawater, usually obscured due to the coexistence of grazers and other bacteria.

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“…On the other hand, the false-negative taxa (51 genera; 2% of the reads) absent from the collection filter could be microbial groups that passed through the 0.22 μm pore-sized filter. As previously reported by Maejima et al (2018), isolated bacteria from lake water samples belonging to the Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria passed through a 0.22 μm pore size filter. The filtered fractions from < 0.2 μm filtered samples that were usually considered "sterile" were found to still contain miniature cells, ultramicrobacteria (i.e., bacteria whose cell size are smaller than 0.1 μm 3 ) and slender filamentous bacteria (e.g., Oligoflexia, Proteobacteria) overlooking a broad diversity of filterable agents (Wang et al, 2007;Nakai 2020).…”

Section: Discussionmentioning

confidence: 92%

Sediment-associated microbial community profiling: sample pre-processing through sequential membrane filtration for 16s rDNA amplicon sequencing

Serrana

Watanabe

2020

Preprint

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Sequential membrane filtration as a pre-processing step for the isolation of microorganisms could provide good quality and integrity DNA that can be preserved and kept at ambient temperatures before community profiling through culture-independent molecular techniques, e.g., 16s rDNA amplicon sequencing. Here, we assessed the impact of pre-processing sediment samples by sequential membrane filtration (from 10, 5 to 0.22 μm pore size membrane filters) for 16s rDNA-based community profiling of sediment-associated microorganisms. Specifically, we examined if there would be method-driven differences between non- and pre-processed sediment samples regarding the quality and quantity of extracted DNA, PCR amplicon, resulting high-throughput sequencing reads, microbial diversity, and community composition. We found no significant difference in the quality and quantity of extracted DNA and PCR amplicons between the two methods. Although we found a significant difference in raw and quality-filtered reads, read abundance after bioinformatics processing (i.e., denoising and the chimeric-read filtering steps) were not significantly different. These results suggest that read abundance after these read processing steps were not influenced by sediment processing or lack thereof. Although the non- and pre-processed sediment samples had more unique than shared amplicon sequence variants (ASVs), we report that their shared ASVs accounted for 74% of both methods' absolute read abundance. More so at the genus level, the final collection filter identified most of the genera (95% of the reads) captured from the non-processed samples, with a total of 51 false-negative (2%) and 59 false-positive genera (3%). Accordingly, the diversity estimates and community composition were not significantly different between the non- and pre-processed samples. We demonstrate that while there were differences in shared and unique taxa, both methods revealed comparable microbial diversity and community composition. We also suggest the inclusion of sequential filters (i.e., pre- and mid-filters) in the community profiling, given the additional taxa not detected from the non-processed and the final collection filter. Our observations highlight the feasibility of pre-processing sediment samples for community analysis and the need to further assess sampling strategies to help conceptualize appropriate study designs for sediment-associated microbial community profiling.

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Proteobacteria and Bacteroidetes are major phyla of filterable bacteria passing through 0.22 μm pore size membrane filter, in Lake Sanaru, Hamamatsu, Japan

Cited by 19 publications

References 22 publications

Isolation and characterization marine bacteria capable of degrading lignin-derived compounds

Isolation and characterization marine bacteria capable of degrading lignin-derived compounds

High growth potential of transiently 0.2-µm-filterable bacteria with extracellular protease activity in coastal seawater

Sediment-associated microbial community profiling: sample pre-processing through sequential membrane filtration for 16s rDNA amplicon sequencing

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