The Bacterial Communities of Full-Scale Biologically Active, Granular Activated Carbon Filters Are Stable and Diverse and Potentially Contain Novel Ammonia-Oxidizing Microorganisms

ABSTRACTThe bacterial community composition of the full-scale biologically active, granular activated carbon (BAC) filters operated at the St. Paul Regional Water Services (SPRWS) was investigated using Illumina MiSeq analysis of PCR-amplified 16S rRNA gene fragments. These bacterial communities were consistently diverse (Shannon index, >4.4; richness estimates, >1,500 unique operational taxonomic units [OTUs]) throughout the duration of the 12-month study period. In addition, only modest shifts in the quantities of individual bacterial populations were observed; of the 15 most prominent OTUs, the most highly variable population (aVariovoraxsp.) modulated less than 13-fold over time and less than 8-fold from filter to filter. The most prominent population in the profiles was aNitrospirasp., representing 13 to 21% of the community. Interestingly, very few of the known ammonia-oxidizing bacteria (AOB; <0.07%) and no ammonia-oxidizingArchaeawere detected in the profiles. Quantitative PCR ofamoAgenes, however, suggested that AOB were prominent in the bacterial communities (amoA/16S rRNA gene ratio, 1 to 10%). We conclude, therefore, that the BAC filters at the SPRWS potentially contained significant numbers of unidentified and novel ammonia-oxidizing microorganisms that possessamoAgenes similar to those of previously described AOB.

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Sponge-Associated Bacteria Are Strictly Maintained in Two Closely Related but Geographically Distant Sponge Hosts

Applied and Environmental Microbiology ◽

10.1128/aem.05285-11 ◽

2011 ◽

Vol 77 (20) ◽

pp. 7207-7216 ◽

Cited By ~ 76

Author(s):

Naomi F. Montalvo ◽

Russell T. Hill

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Bacterial Communities ◽

Sponge Species ◽

Rrna Gene ◽

Gene Sequences ◽

Associated Bacteria ◽

Content Type ◽

Key Species ◽

Sponge Associated Bacteria

ABSTRACTThe giant barrel spongesXestospongiamutaandXestospongiatestudinariaare ubiquitous in tropical reefs of the Atlantic and Pacific Oceans, respectively. They are key species in their respective environments and are hosts to diverse assemblages of bacteria. These two closely related sponges from different oceans provide a unique opportunity to examine the evolution of sponge-associated bacterial communities. Mitochondrial cytochrome oxidase subunit I gene sequences fromX.mutaandX.testudinariashowed little divergence between the two species. A detailed analysis of the bacterial communities associated with these sponges, comprising over 900 full-length 16S rRNA gene sequences, revealed remarkable similarity in the bacterial communities of the two species. Both sponge-associated communities include sequences found only in the twoXestospongiaspecies, as well as sequences found also in other sponge species and are dominated by three bacterial groups,Chloroflexi,Acidobacteria, andActinobacteria. While these groups consistently dominate the bacterial communities revealed by 16S rRNA gene-based analysis of sponge-associated bacteria, the depth of sequencing undertaken in this study revealed clades of bacteria specifically associated with each of the twoXestospongiaspecies, and also with the genusXestospongia, that have not been found associated with other sponge species or other ecosystems. This study, comparing the bacterial communities associated with closely related but geographically distant sponge hosts, gives new insight into the intimate relationships between marine sponges and some of their bacterial symbionts.

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Composition and Variability of Biofouling Organisms in Seawater Reverse Osmosis Desalination Plants

Applied and Environmental Microbiology ◽

10.1128/aem.00122-11 ◽

2011 ◽

Vol 77 (13) ◽

pp. 4390-4398 ◽

Cited By ~ 46

Author(s):

Minglu Zhang ◽

Sunny Jiang ◽

Dian Tanuwidjaja ◽

Nikolay Voutchkov ◽

Eric M. V. Hoek ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Reverse Osmosis ◽

Clone Library ◽

Bacterial Communities ◽

Rrna Gene ◽

Sequencing Analysis ◽

Content Type ◽

Seawater Reverse Osmosis ◽

Desalination Plants

ABSTRACTSeawater reverse osmosis (SWRO) membrane biofouling remains a common challenge in the desalination industry, but the marine bacterial community that causes membrane fouling is poorly understood. Microbial communities at different stages of treatment processes (intake, cartridge filtration, and SWRO) of a desalination pilot plant were examined by both culture-based and culture-independent approaches. Bacterial isolates were identified to match the generaShewanella,Alteromonas,Vibrio, andCellulophagabased on 16S rRNA gene sequencing analysis. The 16S rRNA gene clone library of the SWRO membrane biofilm showed that a filamentous bacterium,Leucothrix mucor, which belongs to the gammaproteobacteria, accounted for nearly 30% of the clone library, while the rest of the microorganisms (61.2% of the total clones) were related to the alphaproteobacteria. 16S rRNA gene terminal restriction fragment length polymorphism (T-RFLP) analysis indicated that bacteria colonizing the SWRO membrane represented a subportion of microbes in the source seawater; however, they were quite different from those colonizing the cartridge filter. The examination of five SWRO membranes from desalination plants located in different parts of the world showed that although the bacterial communities from the membranes were not identical to each other, some dominant bacteria were commonly observed. In contrast, bacterial communities in source seawater were significantly different based on location and season. Microbial profiles from 14 cartridge filters collected from different plants also revealed spatial trends.

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Characterisation and comparison of bacterial communities on reverse osmosis membranes of a full-scale desalination plant by bacterial 16S rRNA gene metabarcoding

npj Biofilms and Microbiomes ◽

10.1038/s41522-017-0021-6 ◽

2017 ◽

Vol 3 (1) ◽

Cited By ~ 18

Author(s):

Veena Nagaraj ◽

Lucy Skillman ◽

Goen Ho ◽

Dan Li ◽

Alexander Gofton

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Reverse Osmosis ◽

Bacterial Communities ◽

Full Scale ◽

Rrna Gene ◽

Desalination Plant ◽

Bacterial 16S Rrna Gene ◽

Reverse Osmosis Membranes

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Molecular characterization of the bacterial communities present in sheep's milk and cheese produced in South Brazilian Region via 16S rRNA gene metabarcoding sequencing

LWT ◽

10.1016/j.lwt.2021.111579 ◽

2021 ◽

Vol 147 ◽

pp. 111579

Author(s):

Creciana M. Endres ◽

Ícaro Maia S. Castro ◽

Laura D. Trevisol ◽

Juliana M. Severo ◽

Michele B. Mann ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Molecular Characterization ◽

Bacterial Communities ◽

Rrna Gene

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Phyllobacterium loti sp. nov. isolated from nodules of Lotus corniculatus

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.052993-0 ◽

2014 ◽

Vol 64 (Pt_3) ◽

pp. 781-786 ◽

Cited By ~ 33

Author(s):

Maximo Sánchez ◽

Martha-Helena Ramírez-Bahena ◽

Alvaro Peix ◽

María J. Lorite ◽

Juan Sanjuán ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Sequence Similarity ◽

Carbon Sources ◽

Lotus Corniculatus ◽

Culture Conditions ◽

Rrna Gene ◽

Content Type ◽

Link Type ◽

The 16S Rrna Gene

Strain S658T was isolated from a Lotus corniculatus nodule in a soil sample obtained in Uruguay. Phylogenetic analysis of the 16S rRNA gene and atpD gene showed that this strain clustered within the genus Phyllobacterium . The closest related species was, in both cases, Phyllobacterium trifolii PETP02T with 99.8 % sequence similarity in the 16S rRNA gene and 96.1 % in the atpD gene. The 16S rRNA gene contains an insert at the beginning of the sequence that has no similarities with other inserts present in the same gene in described rhizobial species. Ubiquinone Q-10 was the only quinone detected. Strain S658T differed from its closest relatives through its growth in diverse culture conditions and in the assimilation of several carbon sources. It was not able to reproduce nodules in Lotus corniculatus. The results of DNA–DNA hybridization, phenotypic tests and fatty acid analyses confirmed that this strain should be classified as a representative of a novel species of the genus Phyllobacterium , for which the name Phyllobacterium loti sp. nov. is proposed. The type strain is S658T( = LMG 27289T = CECT 8230T).

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Faecalicoccus acidiformans gen. nov., sp. nov., isolated from the chicken caecum, and reclassification of Streptococcus pleomorphus (Barnes et al. 1977), Eubacterium biforme (Eggerth 1935) and Eubacterium cylindroides (Cato et al. 1974) as Faecalicoccus pleomorphus comb. nov., Holdemanella biformis gen. nov., comb. nov. and Faecalitalea cylindroides gen. nov., comb. nov., respectively, within the family Erysipelotrichaceae

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.064626-0 ◽

2014 ◽

Vol 64 (Pt_11) ◽

pp. 3877-3884 ◽

Cited By ~ 50

Author(s):

Celine De Maesschalck ◽

Filip Van Immerseel ◽

Venessa Eeckhaut ◽

Siegrid De Baere ◽

Margo Cnockaert ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Type Species ◽

Gene Sequence ◽

Sequence Similarity ◽

16S Rrna Gene Sequence ◽

Rrna Gene ◽

Rrna Gene Sequence ◽

Content Type ◽

Link Type

Strains LMG 27428T and LMG 27427 were isolated from the caecal content of a chicken and produced butyric, lactic and formic acids as major metabolic end products. The genomic DNA G+C contents of strains LMG 27428T and LMG 27427 were 40.4 and 38.8 mol%. On the basis of 16S rRNA gene sequence similarity, both strains were most closely related to the generically misclassified Streptococcus pleomorphus ATCC 29734T. Strain LMG 27428T could be distinguished from S. pleomorphus ATCC 29734T based on production of more lactic acid and less formic acid in M2GSC medium, a higher DNA G+C content and the absence of activities of acid phosphatase and leucine, arginine, leucyl glycine, pyroglutamic acid, glycine and histidine arylamidases, while strain LMG 27428 was biochemically indistinguishable from S. pleomorphus ATCC 29734T. The novel genus Faecalicoccus gen. nov. within the family Erysipelotrichaceae is proposed to accommodate strains LMG 27428T and LMG 27427. Strain LMG 27428T ( = DSM 26963T) is the type strain of Faecalicoccus acidiformans sp. nov., and strain LMG 27427 ( = DSM 26962) is a strain of Faecalicoccus pleomorphus comb. nov. (type strain LMG 17756T = ATCC 29734T = DSM 20574T). Furthermore, the nearest phylogenetic neighbours of the genus Faecalicoccus are the generically misclassified Eubacterium cylindroides DSM 3983T (94.4 % 16S rRNA gene sequence similarity to strain LMG 27428T) and Eubacterium biforme DSM 3989T (92.7 % 16S rRNA gene sequence similarity to strain LMG 27428T). We present genotypic and phenotypic data that allow the differentiation of each of these taxa and propose to reclassify these generically misnamed species of the genus Eubacterium formally as Faecalitalea cylindroides gen. nov., comb. nov. and Holdemanella biformis gen. nov., comb. nov., respectively. The type strain of Faecalitalea cylindroides is DSM 3983T = ATCC 27803T = JCM 10261T and that of Holdemanella biformis is DSM 3989T = ATCC 27806T = CCUG 28091T.

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Pseudoseohaeicola caenipelagi gen. nov., sp. nov., isolated from a tidal flat

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.000182 ◽

2015 ◽

Vol 65 (Pt_6) ◽

pp. 1819-1824 ◽

Cited By ~ 15

Author(s):

Sooyeon Park ◽

Ji-Min Park ◽

Chul-Hyung Kang ◽

Song-Gun Kim ◽

Jung-Hoon Yoon

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Tidal Flat ◽

Type Strain ◽

Type Species ◽

Phylogenetic Trees ◽

Sequence Similarity ◽

Rrna Gene ◽

Content Type ◽

Link Type

A Gram-stain-negative, non-motile, aerobic and pleomorphic bacterium, designated BS-W13T, was isolated from a tidal flat on the South Sea, South Korea, and its taxonomic position was investigated using a polyphasic approach. Strain BS-W13T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 1.0–2.0 % (w/v) NaCl. Neighbour-joining and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain BS-W13T clustered with the type strain of Seohaeicola saemankumensis , showing the highest sequence similarity (95.96 %) to this strain. Strain BS-W13T exhibited 16S rRNA gene sequence similarity values of 95.95, 95.91, 95.72 and 95.68 % to the type strains of Sulfitobacter donghicola , Sulfitobacter porphyrae , Sulfitobacter mediterraneus and Roseobacter litoralis , respectively. Strain BS-W13T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The polar lipid profile of strain BS-W13T, containing phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid as major components, was distinguishable from those of some phylogenetically related taxa. The DNA G+C content of strain BS-W13T was 58.1 mol%. The phylogenetic data and differential chemotaxonomic and other phenotypic properties revealed that strain BS-W13T constitutes a novel genus and species within family Rhodobacteraceae of the class Alphaproteobacteria , for which the name Pseudoseohaeicola caenipelagi gen. nov., sp. nov. is proposed. The type strain is BS-W13T ( = KCTC 42349T = CECT 8724T).

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The Western Progression of Lyme Disease: Infectious and NonclonalBorrelia burgdorferi Sensu LatoPopulations in Grand Forks County, North Dakota

Applied and Environmental Microbiology ◽

10.1128/aem.02422-14 ◽

2014 ◽

Vol 81 (1) ◽

pp. 48-58 ◽

Cited By ~ 12

Author(s):

Brandee L. Stone ◽

Nathan M. Russart ◽

Robert A. Gaultney ◽

Angela M. Floden ◽

Jefferson A. Vaughan ◽

...

Keyword(s):

Lyme Disease ◽

16S Rrna ◽

16S Rrna Gene ◽

North Dakota ◽

Intergenic Spacer ◽

Rrna Gene ◽

Content Type ◽

Intergenic Spacer Region ◽

Grand Forks ◽

The 16S Rrna Gene

ABSTRACTScant attention has been paid to Lyme disease,Borrelia burgdorferi,Ixodes scapularis, or reservoirs in eastern North Dakota despite the fact that it borders high-risk counties in Minnesota. Recent reports ofB. burgdorferiandI. scapularisin North Dakota, however, prompted a more detailed examination. Spirochetes cultured from the hearts of five rodents trapped in Grand Forks County, ND, were identified asB. burgdorferi sensu latothrough sequence analyses of the 16S rRNA gene, the 16S rRNA gene-ileTintergenic spacer region,flaB,ospA,ospC, andp66. OspC typing revealed the presence of groups A, B, E, F, L, and I. Two rodents were concurrently carrying multiple OspC types. Multilocus sequence typing suggested the eastern North Dakota strains are most closely related to those found in neighboring regions of the upper Midwest and Canada. BALB/c mice were infected withB. burgdorferiisolate M3 (OspC group B) by needle inoculation or tick bite. Tibiotarsal joints and ear pinnae were culture positive, andB. burgdorferiM3 was detected by quantitative PCR (qPCR) in the tibiotarsal joints, hearts, and ear pinnae of infected mice. Uninfected larvalI. scapularisticks were able to acquireB. burgdorferiM3 from infected mice; M3 was maintained inI. scapularisduring the molt from larva to nymph; and further, M3 was transmitted from infectedI. scapularisnymphs to naive mice, as evidenced by cultures and qPCR analyses. These results demonstrate that isolate M3 is capable of disseminated infection by both artificial and natural routes of infection. This study confirms the presence of unique (nonclonal) and infectiousB. burgdorferipopulations in eastern North Dakota.

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Sphingobacterium yanglingense sp. nov., isolated from the nodule surface of soybean

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.068254-0 ◽

2014 ◽

Vol 64 (Pt_11) ◽

pp. 3862-3866 ◽

Cited By ~ 20

Author(s):

Shi Peng ◽

Dong Dan Hong ◽

Yang Bing Xin ◽

Li Ming Jun ◽

Wei Ge Hong

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Polar Lipids ◽

Rrna Gene ◽

Content Type ◽

Link Type ◽

Gram Staining ◽

Physiological And Biochemical Characteristics ◽

Gene Sequence Analysis ◽

Type Strains

A Gram-staining-negative, non-motile, catalase- and oxidase-positive strain, designated CCNWSP36-1T, was isolated from the nodule surface of soybean [Glycine max (L.) Merrill] cultivar Zhonghuang 13. The 16S rRNA gene sequence analysis clearly showed that the isolate represented a member of the genus Sphingobacterium . On the basis of pairwise comparisons of 16S rRNA gene sequences, strain CCNWSP36-1T showed 96.8 % similarity to Sphingobacterium nematocida CCTCC AB 2010390T and less than 95.2 % similarity to other members of the genus Sphingobacterium . Growth of strain CCNWSP36-1T occurred at 10–40 °C and at pH 5.0–9.0. The NaCl range (w/v) for growth was 0–4 %. The predominant isoprenoid quinone was MK-7. The polar lipids were phosphatidylethanolamine and several unidentified polar lipids. Sphingolipid was present. The major fatty acids were iso-C15 : 0 and summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c). The G+C content of the genomic DNA was 41.1 mol%. As the physiological and biochemical characteristics of strain CCNWSP36-1T and the type strains of its closest phylogenetic neighbours showed clear differences, a novel species, Sphingobacterium yanglingense, is proposed. The type strain is CCNWSP36-1T ( = ACCC 19328T = JCM 30166T).

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