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Microbes and Environments

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https://www.readbyqxmd.com/read/29910221/assessment-of-capacity-to-capture-dna-aerosols-by-clean-filters-for-molecular-biology-experiments
#1
Yuki Morono, Tatsuhiko Hoshino, Takeshi Terada, Taketo Suzuki, Takahiro Sato, Hisashi Yuasa, Yuji Kubota, Fumio Inagaki
Experimental contamination by exogenous DNA is a major issue in molecular biological studies for data quality and its management. We herein assessed DNA aerosols for the risk of contamination and tested the capacity of clean air filters to trap and remove DNA aerosols. DNA aerosols were generated by atomizing a DNA solution and introduced into a laminar flow clean air unit. Capture and detection performed upstream and downstream of the clean air unit showed that a significant fraction (>99.96%) of introduced molecules was trapped and removed by the filter...
June 16, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29910220/flow-cytometry-for-rapid-enumeration-and-biomass-quantification-of-thraustochytrids-in-coastal-seawaters
#2
Yingbo Duan, Biswarup Sen, Ningdong Xie, James S Paterson, Zixi Chen, Guangyi Wang
Marine fungus-like eukaryotic unicellular protists (thraustochytrids) are considered to play an important role in the marine microbial food web. However, their abundance, distribution, and relative biomass in coastal waters have not yet been examined in detail. By using a flow cytometry method (FCM) for the rapid enumeration of thraustochytrids in nearshore and offshore stations along the Gulf of Bohai, China, we herein expanded current knowledge on their ecological significance. The FCM method allows for the rapid detection and quantification of prokaryotic and eukaryotic cells, but is rarely applied to the enumeration of small eukaryotic protists...
June 16, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29910219/chitin-increases-mycobacterium-ulcerans-growth-in-acidic-environments
#3
Daniel Sanhueza, Christine Chevillon, Nicolas Bouzinbi, Sylvain Godreuil, Jean-François Guégan
Species with a chitinous exoskeleton are overrepresented among the aquatic organisms carrying Mycobacterium ulcerans (MU) in nature and laboratory experiments have demonstrated the enhancing effects of chitin on the growth of MU. Field surveys identified pH as one of the key parameters delineating the distribution of MU in tropical regions. The present study investigated the relationship between chitin and pH in MU growth. By focusing on pH variations in the field, our results revealed that chitin enhanced MU growth in acidic environments...
June 16, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29899169/geochemical-and-microbiological-evidence-for-microbial-methane-production-in-deep-aquifers-of-the-cretaceous-accretionary-prism
#4
Makoto Matsushita, Kenta Magara, Yu Sato, Naoya Shinzato, Hiroyuki Kimura
Accretionary prisms are thick layers of sedimentary material piled up at convergent plate boundaries. Large amounts of anaerobic groundwater and methane (CH4 ) are contained in the deep aquifers associated with accretionary prisms. In order to identify microbial activity and CH4 production processes in the deep aquifers associated with the Cretaceous accretionary prism in Okinawa Island, Japan, we performed geochemical and microbiological studies using anaerobic groundwater and natural gas (mainly CH4 ) samples collected through four deep wells...
June 13, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29794413/co-occurrence-network-reveals-the-higher-fragmentation-of-the-bacterial-community-in-kaidu-river-than-its-tributaries-in-northwestern-china
#5
Yang Hu, Chengrong Bai, Jian Cai, Jiangyu Dai, Keqiang Shao, Xiangming Tang, Guang Gao
Rivers and their tributaries sculpt the earth's surface, and play an important role in substance circulation and energy flow. Bacteria are involved in most biogeochemical processes in the fluvial ecosystem; however, their pattern distribution in a river and its tributaries has not yet been investigated in detail. In the present study, high-throughput sequencing was employed to examine bacterial communities and their co-occurrence networks between Kaidu River and its nine tributaries in northwestern China. The results obtained demonstrated that both bacterial communities shared a similar dominant sub-community, mainly consisting of Actinobacteria, Bacteroidetes, and Proteobacteria, with Limnohabitans and Variovorax as the dominant genera...
May 22, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29760298/a-newly-designed-primer-revealed-high-phylogenetic-diversity-of-endozoicomonas-in-coral-reefs
#6
Jia-Ho Shiu, Jiun-Yan Ding, Ching-Hung Tseng, Shueh-Ping Lou, Takuma Mezaki, Yu-Ting Wu, Hsiang-Iu Wang, Sen-Lin Tang
Endozoicomonas bacteria are commonly regarded as having a potentially symbiotic relationship with their coral hosts. However, their diversity and phylogeny in samples collected from various sources remain unclear. Therefore, we designed an Endozoicomonas-specific primer paired with a bacterial universal primer to detect the 16S ribosomal RNA (rRNA) genes of this taxon and conducted an in-depth investigation of the Endozoicomonas community structure in reef-building corals. The primer had high specificity in the V3-V4 region (95...
May 12, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29709896/ureolytic-prokaryotes-in-soil-community-abundance-and-diversity
#7
Mamoru Oshiki, Mitsuru Araki, Yuga Hirakata, Masashi Hatamoto, Takashi Yamaguchi, Nobuo Araki
Although the turnover of urea is a crucial process in nitrogen transformation in soil, limited information is currently available on the abundance and diversity of ureolytic prokaryotes. The abundance and diversity of the soil 16S rRNA gene and ureC (encoding a urease catalytic subunit) were examined in seven soil types using quantitative PCR and amplicon sequencing with Illumina MiSeq. The amplicon sequencing of ureC revealed that the ureolytic community was composed of phylogenetically varied prokaryotes, and we detected 363 to 1,685 species-level ureC operational taxonomic units (OTUs) per soil sample, whereas 5,984 OTUs were site-specific OTUs found in only one of the seven soil types...
April 28, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29709895/importance-of-soil-temperature-for-the-growth-of-temperate-crops-under-a-tropical-climate-and-functional-role-of-soil-microbial-diversity
#8
Nurul Syazwani Ahmad Sabri, Zuriati Zakaria, Shaza Eva Mohamad, A Bakar Jaafar, Hirofumi Hara
A soil cooling system that prepares soil for temperate soil temperatures for the growth of temperate crops under a tropical climate is described herein. Temperate agriculture has been threatened by the negative impact of temperature increases caused by climate change. Soil temperature closely correlates with the growth of temperate crops, and affects plant processes and soil microbial diversity. The present study focuses on the effects of soil temperatures on lettuce growth and soil microbial diversity that maintains the growth of lettuce at low soil temperatures...
April 28, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29887548/influence-of-the-chemical-form-of-antimony-on-soil-microbial-community-structure-and-arsenite-oxidation-activity
#9
Takafumi Kataoka, Satoshi Mitsunobu, Natsuko Hamamura
In the present study, the influence of the co-contamination with various chemical forms of antimony (Sb) with arsenite (As[III]) on soil microbial communities was investigated. The oxidation of As(III) to As(V) was monitored in soil columns amended with As(III) and three different chemical forms of Sb: antimony potassium tartrate (Sb[III]-tar), antimony(III) oxide (Sb2 O3 ), and potassium antimonate (Sb[V]). Soil microbial communities were examined qualitatively and quantitatively using 16S rDNA- and arsenite oxidase gene (aioA)-targeted analyses...
July 4, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29863059/host-specific-bacteroides-markers-based-microbial-source-tracking-in-aquaculture-areas
#10
Hye Young Ko, Kyuseon Cho, SungJun Park, Jin Hwi Kim, Joo-Hyon Kang, Yong Seok Jeong, Jong Duck Choi, Yongsik Sin, Cheonghoon Lee, GwangPyo Ko
Various waterborne pathogens originate from human or animal feces and may cause severe gastroenteric outbreaks. Bacteroides spp. that exhibit strong host- or group-specificities are promising markers for identifying fecal sources and their origins. In the present study, 240 water samples were collected from two major aquaculture areas in Republic of Korea over a period of approximately 1 year, and the concentrations and occurrences of four host-specific Bacteroides markers (human, poultry, pig, and ruminant) were evaluated in the study areas...
July 4, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29863058/a-new-primer-set-to-amplify-the-mitochondrial-cytochrome-c-oxidase-subunit-i-coi-gene-in-the-dha-rich-microalgae-the-genus-aurantiochytrium
#11
Goh Nishitani, Masaki Yoshida
This study was performed in order to develop a primer set for mitochondrial cytochrome c oxidase subunit I (COI) in the DHA-rich microalgae of the genus Aurantiochytrium. The performance of the primer set was tested using 12 Aurantiochytrium strains and other thraustochytrid species. There were no genetic polymorphisms in the mitochondrial sequences from the Aurantiochytrium strains, in contrast to the nuclear 18S rRNA gene sequence. This newly developed primer set amplified sequences from Aurantiochytrium and closely related genera, and may be useful for species identification and clarifying the genetic diversity of Aurantiochytrium in the field...
July 4, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29848838/composition-and-diversity-of-soil-fungi-in-dipterocarpaceae-dominated-seasonal-tropical-forests-in-thailand
#12
Sarasa Amma, Hirokazu Toju, Chongrak Wachrinrat, Hirotoshi Sato, Akifumi S Tanabe, Taksin Artchawakom, Mamoru Kanzaki
Although fungi play essential roles in nutrient cycles and plant growth in forest ecosystems, limited information is currently available on the community compositions of soil fungi in tropical forests. Few studies have examined fungal community structures in seasonal tropical forests, in which forest fires potentially have a large impact on above- and belowground community processes. Based on high-throughput sequencing technologies, we herein examined the diversity and community structures of soil fungi in dry seasonal tropical forests in Sakaerat, northeast Thailand...
July 4, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29806626/taxon-richness-of-megaviridae-exceeds-those-of-bacteria-and-archaea-in-the-ocean
#13
Tomoko Mihara, Hitoshi Koyano, Pascal Hingamp, Nigel Grimsley, Susumu Goto, Hiroyuki Ogata
Since the discovery of the giant mimivirus, evolutionarily related viruses have been isolated or identified from various environments. Phylogenetic analyses of this group of viruses, tentatively referred to as the family "Megaviridae", suggest that it has an ancient origin that may predate the emergence of major eukaryotic lineages. Environmental genomics has since revealed that Megaviridae represents one of the most abundant and diverse groups of viruses in the ocean. In the present study, we compared the taxon richness and phylogenetic diversity of Megaviridae, Bacteria, and Archaea using DNA-dependent RNA polymerase as a common marker gene...
July 4, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29806625/microbial-diversity-in-sediments-from-the-bottom-of-the-challenger-deep-the-mariana-trench
#14
Takuro Nunoura, Manabu Nishizawa, Miho Hirai, Shigeru Shimamura, Phurt Harnvoravongchai, Osamu Koide, Yuki Morono, Toshiaki Fukui, Fumio Inagaki, Junichi Miyazaki, Yoshihiro Takaki, Ken Takai
The Challenger Deep is the deepest ocean on Earth. The present study investigated microbial community structures and geochemical cycles associated with the trench bottom sediments of the Challenger Deep, the Mariana Trench. The SSU rRNA gene communities found in trench bottom sediments were dominated by the bacteria Chloroflexi (SAR202 and other lineages), Bacteroidetes, Planctomycetes, "Ca. Marinimicrobia" (SAR406), and Gemmatimonadetes and by the archaeal α subgroup of MGI Thaumarchaeota and "Ca...
July 4, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29681561/bacterial-community-in-water-and-air-of-two-sub-alpine-lakes-in-taiwan
#15
Kshitij Tandon, Shan-Hua Yang, Min-Tao Wan, Chia-Chin Yang, Bayanmunkh Baatar, Chih-Yu Chiu, Jeng-Wei Tsai, Wen-Cheng Liu, Sen-Lin Tang
Very few studies have attempted to profile the microbial communities in the air above freshwater bodies, such as lakes, even though freshwater sources are an important part of aquatic ecosystems and airborne bacteria are the most dispersible microorganisms on earth. In the present study, we investigated microbial communities in the waters of two high mountain sub-alpine montane lakes-located 21 km apart and with disparate trophic characteristics-and the air above them. Although bacteria in the lakes had locational differences, their community compositions remained constant over time...
April 21, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29553064/presence-of-a-haloarchaeal-halorhodopsin-like-cl-pump-in-marine-bacteria
#16
Yu Nakajima, Takashi Tsukamoto, Yohei Kumagai, Yoshitoshi Ogura, Tetsuya Hayashi, Jaeho Song, Takashi Kikukawa, Makoto Demura, Kazuhiro Kogure, Yuki Sudo, Susumu Yoshizawa
Light-driven ion-pumping rhodopsins are widely distributed among bacteria, archaea, and eukaryotes in the euphotic zone of the aquatic environment. H+ -pumping rhodopsin (proteorhodopsin: PR), Na+ -pumping rhodopsin (NaR), and Cl- -pumping rhodopsin (ClR) have been found in marine bacteria, which suggests that these genes evolved independently in the ocean. Putative microbial rhodopsin genes were identified in the genome sequences of marine Cytophagia. In the present study, one of these genes was heterologously expressed in Escherichia coli cells and the rhodopsin protein named Rubricoccus marinus halorhodopsin (RmHR) was identified as a light-driven inward Cl- pump...
March 29, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29540639/different-metabolomic-responses-to-carbon-starvation-between-light-and-dark-conditions-in-the-purple-photosynthetic-bacterium-rhodopseudomonas-palustris
#17
Nanako Kanno, Katsumi Matsuura, Shin Haruta
Purple photosynthetic bacteria utilize light energy for growth. We previously demonstrated that light energy contributed to prolonging the survival of multiple purple bacteria under carbon-starved conditions. In order to clarify the effects of illumination on metabolic states under carbon-starved, non-growing conditions, we herein compared the metabolic profiles of starved cells in the light and dark using the purple bacterium, Rhodopseudomonas palustris. The metabolic profiles of starved cells in the light were markedly different from those in the dark...
March 29, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29540638/comparative-genomic-insights-into-endofungal-lifestyles-of-two-bacterial-endosymbionts-mycoavidus-cysteinexigens-and-burkholderia-rhizoxinica
#18
Dilruba Sharmin, Yong Guo, Tomoyasu Nishizawa, Shoko Ohshima, Yoshinori Sato, Yusuke Takashima, Kazuhiko Narisawa, Hiroyuki Ohta
Endohyphal bacteria (EHB), dwelling within fungal hyphae, markedly affect the growth and metabolic potential of their hosts. To date, two EHB belonging to the family Burkholderiaceae have been isolated and characterized as new taxa, Burkholderia rhizoxinica (HKI 454T ) and Mycoavidus cysteinexigens (B1-EBT ), in Japan. Metagenome sequencing was recently reported for Mortierella elongata AG77 together with its endosymbiont M. cysteinexigens (Mc-AG77) from a soil/litter sample in the USA. In the present study, we elucidated the complete genome sequence of B1-EBT and compared it with those of Mc-AG77 and HKI 454T ...
March 29, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29491247/differential-distribution-of-salmonella-serovars-and-campylobacter-spp-isolates-in-free-living-crows-and-broiler-chickens-in-aomori-japan
#19
Masashi Okamura, Miyuki Kaneko, Shinjiro Ojima, Hiroki Sano, Junji Shindo, Hiroaki Shirafuji, Satomi Yamamoto, Taishi Tanabe, Yasuhiro Yoshikawa, Dong-Liang Hu
Salmonella and Campylobacter cause foodborne enteritis mainly via the consumption of raw/undercooked contaminated poultry meat and products. Broiler flocks are primarily colonized with these bacteria; however, the underlying etiology remains unclear. The present study was conducted in order to obtain further information on the prevalence and genotypic distribution of Salmonella and Campylobacter in free-living crows and broiler flocks in a region for 2 years, thereby facilitating estimations of the potential risk of transmission of C...
March 29, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29479006/plant-materials-are-sustainable-substrates-supporting-new-technologies-of-plant-only-based-culture-media-for-in-vitro-culturing-of-the-plant-microbiota
#20
Elhussein F Mourad, Mohamed S Sarhan, Hassan-Sibroe A Daanaa, Mennatullah Abdou, Ahmed T Morsi, Mohamed R Abdelfadeel, Hend Elsawey, Rahma Nemr, Mahmoud El-Tahan, Mervat A Hamza, Mohamed Abbas, Hanan H Youssef, Abdelhadi A Abdelhadi, Wafaa M Amer, Mohamed Fayez, Silke Ruppel, Nabil A Hegazi
In order to improve the culturability and biomass production of rhizobacteria, we previously introduced plant-only-based culture media. We herein attempted to widen the scope of plant materials suitable for the preparation of plant-only-based culture media. We chemically analyzed the refuse of turfgrass, cactus, and clover. They were sufficiently rich to support good in vitro growth by rhizobacteria isolates representing Proteobacteria and Firmicutes. They were also adequate and efficient to produce a cell biomass in liquid batch cultures...
March 29, 2018: Microbes and Environments
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