The Family Planococcaceae

Shivaji, Sisinthy; Srinivas, T. N. R.; Reddy, G. S. N.

doi:10.1007/978-3-642-30120-9_351

“…Khawia japonensis had a significant positive correlation with U114 , Epulopiscium , Bacteroides , Clostridium , Peptostreptococcaceae , Rummeliibacillus , Lysinibacillus boronitolerans , Marinibacillus and Chitinilyticum in our study. U114 might have a role in the regulation of bile acids metabolism [50]; Epulopiscium may be able to break down carbohydrates and complex hemicellulose [51]; Bacteroides has a capacity of breaking down polysaccharides [52]; Clostridium ferments polysaccharides and proteins to produce alcohols and short-chain fatty acids [53]; Peptostreptococcaceae can utilize proteinaceous substrates and carbohydrates [54]; Rummeliibacillus can hydrolyze gelatin and produce acids [55]; Lysinibacillus boronitolerans produces nitrilase, converses iminodiacetonitrile (IDAN) to iminodiacetic acid (IDA) [56], and degrades ioxynil octanoate herbicide [57]; Marinibacillus utilizes cellobiose, trehalose and xylose [58]; and finally, Chitinilyticum degrades chitin [59]. All these microbial taxa are very important for the digestion of polysaccharides and proteins.…”

Section: Discussionmentioning

confidence: 99%

Effect of intestinal tapeworms on the gut microbiota of the common carp, Cyprinus carpio

Fu

¹

,

Xiong

²

,

Feng

³

et al. 2019

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Background Parasitic protozoans, helminths, alter the gut microbiota in mammals, yet little is known about the influence of intestinal cestodes on gut microbiota in fish. In the present study, the composition and diversity of the hindgut microbiota were determined in the intestine of common carp ( Cyprinus carpio ) infected with two tapeworm species, Khawia japonensis and Atractolytocestus tenuicollis . Results The intestine contained a core microbiota composed of Proteobacteria, Fusobacteria and Tenericutes. Infection with the two cestode species had no significant effect on the microbial diversity and richness, but it altered the microbial composition at the genus level. PCoA analysis indicated that microbial communities in the infected and uninfected common carp could not be distinguished from each other. However, a Mantel test indicated that the abundance of K. japonensis was significantly correlated with the microbial composition ( P = 0.015), while the abundance of A. tenuicollis was not ( P = 0.954). According to Pearsonʼs correlation analysis, the abundance of K. japonensis exhibited an extremely significant ( P < 0.001) positive correlation with the following gut microbiota taxa: Epulopiscium , U114 , Bacteroides , Clostridium and Peptostreptococcaceae (0.8< r < 0.9); and a significant ( P < 0.05) correlation with Enterobacteriaceae , Micrococcaceae , Rummeliibacillus , Lysinibacillus boronitolerans , Veillonellaceae , Oxalobacteraceae , Aeromonadaceae (negative), Marinibacillus and Chitinilyticum (0.4< r < 0.7). Conclusions These results suggest that the composition of gut microbiota was somewhat affected by the K. japonensis infection. Additionally, increased ratios of pathogenic bacteria ( Lawsonia and Plesiomonas ) were also associated with the K. japonensis infection, which may therefore increase the likelihood of disease. Electronic supplementary material The online version of this article (10.1186/s13071-019-3510-z) contains supplementary material, which is available to authorized users.

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“…While Planococcus has previously been found at a North Sea beach in England (Engelhardt et al, 2001), Planomicrobium was reported to be present in marine sediments in China (Dai et al, 2005). They are aerobic or facultative anaerobic with some being able to reduce nitrate (Shivaji et al, 2014).…”

Section: Deeper Penetration Of O 2 and No 3 Lead To A Subsurface Bloomentioning

confidence: 96%

Seasonal Dynamics of Microbial Diversity at a Sandy High Energy Beach Reveal a Resilient Core Community

Degenhardt

¹

,

Dlugosch

²

,

Ahrens

³

et al. 2020

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Sandy beaches have received increasing attention due to their global ubiquity and ecological services they provide. Previous investigations on their microbial diversity mostly targeted low energy beaches, lacked seasonality or geochemical information. We now have used a multidisciplinary approach to study the microbial diversity within sediments of a sandy, high energy beach that additionally exhibits submarine groundwater discharge (SGD) in the intertidal. We sampled two transects at three seasons down to a depth of one meter for 16S rRNA gene amplicon sequencing and subsequent correlation of microbial diversity to physico-chemical parameters. We found that advection driven transport of porewater constituents and constant physical reworking of the sediments prevented a distinct formation of vertically stratified redox zones. Consequently, a uniform microbial core community of generalists established independently of sampling site and depth. During spring, the community structure was disturbed by a "subsurface bloom" of Bacteroidetes and Firmicutes, probably due to deeper oxygen and nitrate penetration depths. In summer, the community returned to its equilibrium state with imprints of the subsurface bloom still visible. In our study, we did not detect a clear impact of SGD on microbial diversity, but found an unexpected homogeneous composition and resilience of the microbial community structure.

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“…Several genera, families and orders have been created on the basis of phylogenetic analyses and the presence of unique signatures in the 16S rRNA gene sequence (Stackebrandt et al, 1997;Ash et al, 1991;Reddy & Garcia-Pichel, 2009;Ivanova et al, 2004;Gauthier et al, 1995;MacDonell & Colwell, 1985;Reddy, 2013), further implying that phylogenetic evidence alone is sufficient to create higher taxonomic ranks. Additionally, discrepancies in phenotypic traits are well documented among species of several genera (Reddy et al, 2013;Shivaji et al, 2013), thus making it difficult to find congruence between phylogeny and expressed characteristics. For example, the genus Glaciecola was described based on arbitrary differences that it exhibited from closely related genera with respect to the nature of habitat, pigmentation, cellular morphology, psychrophilic growth, requirement for salt and oxygen and the presence of polyunsaturated fatty acids (Bowman et al, 1998), none of which are genus-specific traits.…”

Section: Phylogenetic Analyses Of the Genus Glaciecolamentioning

confidence: 99%

Phylogenetic analyses of the genus Glaciecola: emended description of the genus Glaciecola, transfer of Glaciecola mesophila, G. agarilytica, G. aquimarina, G. arctica, G. chathamensis, G. polaris and G. psychrophila to the genus Paraglaciecola gen. nov. as Paraglaciecola mesophila comb. nov., P. agarilytica comb. nov., P. aquimarina comb. nov., P. arctica comb. nov., P. chathamensis comb. nov., P. polaris comb. nov. and P. psychrophila comb. nov., and description of Paraglaciecola oceanifecundans sp. nov.

Shivaji

¹

,

Reddy

²

2014

International Journal of Systematic and Evolutionary Microbiology

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Phylogenetic analyses of the genus Glaciecola were performed using the sequences of the 16S rRNA gene and the GyrB protein to establish its taxonomic status. The results indicated a consistent clustering of the genus Glaciecola into two clades, with significant bootstrap values, with all the phylogenetic methods employed. Clade 1 was represented by seven species, Glaciecola agarilytica , G. aquimarina , G. arctica , G. chathamensis , G. mesophila , G. polaris and G. psychrophila , while clade 2 consisted of only three species, Glaciecola nitratireducens , G. pallidula and G. punicea . Evolutionary distances between species of clades 1 and 2, based on 16S rRNA gene and GyrB protein sequences, ranged from 93.0 to 95.0 % and 69.0 to 73.0 %, respectively. In addition, clades 1 and 2 possessed 18 unique signature nucleotides, at positions 132, 184 : 193, 185 : 192, 230, 616 : 624, 631, 632, 633, 738, 829, 1257, 1265, 1281, 1356 and 1366, in the 16S rRNA gene sequence and can be differentiated by the occurrence of a 15 nt signature motif 5′-CAAATCAGAATGTTG at positions 1354–1368 in members of clade 2. Robust clustering of the genus Glaciecola into two clades based on analysis of 16S rRNA gene and GyrB protein sequences, 16S rRNA gene sequence similarity of ≤95.0 % and the occurrence of signature nucleotides and signature motifs in the 16S rRNA gene suggested that the genus should be split into two genera. The genus Paraglaciecola gen. nov. is therefore created to accommodate the seven species of clade 1, while the name Glaciecola sensu stricto is retained to represent species of clade 2. The species of clade 1 are transferred to the genus Paraglaciecola as Paraglaciecola mesophila comb. nov. (type strain DSM 15026T = KMM 241T), P. agarilytica comb. nov. (type strain NO2T = KCTC 12755T = LMG 23762T), P. aquimarina comb. nov. (type strain GGW-M5T = KCTC 32108T = CCUG 62918T), P. arctica comb. nov. (type strain BSs20135T = CCTCC AB 209161T = KACC 14537T), P. chathamensis comb. nov. (type strain E3T = CGMCC 1.7001T = JCM 15139T), P. polaris comb. nov. (type strain ARK 150T = CIP 108324T = LMG 21857T) and P. psychrophila comb. nov. (type strain 170T = CGMCC1.6130T = JCM 13954T). The type species of the genus Paraglaciecola is Paraglaciecola mesophila. An emended description of the genus Glaciecola is provided. In addition, a novel strain, 162Z-12T, was isolated from seawater collected as part of an iron fertilization experiment (LOHAFEX) conducted in the Southern Ocean in 2009 and was subjected to polyphasic taxonomic characterization. Cells of 162Z-12T were Gram-negative, aerobic, motile, ovoid to short rod-shaped, obligatorily halophilic and possessed all the characteristics of the genus Paraglaciecola. Strain 162Z-12T shared the highest 16S rRNA gene sequence similarity with the type strains of P. agarilytica (99.7 %), P. chathamensis (99.7 %), P. mesophila (98.5 %) and P. polaris (98.3 %). However, it exhibited DNA–DNA relatedness of less than 70.0 % with its nearest phylogenetic relatives, well below the threshold value for species delineation. Further, strain 162Z-12T differed from the nearest species in several phenotypic characteristics, in addition to the occurrence of unique nucleotides G, T, T and T at positions 1194, 1269, 1270 and 1271 of the 16S rRNA gene. Based on the cumulative differences it exhibited from its nearest phylogenetic neighbours, strain 162Z-12T was identified as a novel member of the genus Paraglaciecola and assigned to the novel species Paraglaciecola oceanifecundans sp. nov. The type strain of Paraglaciecola oceanifecundans is 162Z-12T ( = KCTC 32337T = LMG 27453T).

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The Family Planococcaceae

Cited by 24 publications

References 199 publications

Effect of intestinal tapeworms on the gut microbiota of the common carp, Cyprinus carpio

Effect of intestinal tapeworms on the gut microbiota of the common carp, Cyprinus carpio

Seasonal Dynamics of Microbial Diversity at a Sandy High Energy Beach Reveal a Resilient Core Community

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