Salinicoccus salitudinis sp. nov., a new moderately halophilic bacterium isolated from a saline soil sample

Phylogenomic and molecular markers based studies on Staphylococcaceae and Gemella species. Proposals for an emended family Staphylococcaceae and three new families (Abyssicoccaceae fam. nov., Salinicoccaceae fam. nov. and Gemellaceae fam. nov.) harboring four new genera, Lacicoccus gen. nov., Macrococcoides gen. nov., Gemelliphila gen. nov., and Phocicoccus gen. nov

The family Staphylococcacae and genus Gemella contain several organisms of clinical or biotechnological importance. We report here comprehensive phylogenomic and comparative analyses on 112 available genomes from species in these taxa to clarify their evolutionary relationships and classification. In a phylogenomic tree based on 678 core proteins, Gemella species were separated from Staphylococcacae by a long branch indicating that they constitute a distinct family (Gemellaceae fam. nov.). In this tree, Staphylococcacae species formed two main clades, one encompassing the genera Aliicoccus, Jeotgalicoccus, Nosocomiicoccus and Salinicoccus (Family "Salinicoccaceae"), while the other clade consisted of the genera Macrococcus, Mammaliicoccus and Staphylococcus (Family Staphylococcaceae emend.). In this tree, species from the genera Gemella, Jeotgalicoccus, Macrococcus and Salinicoccus each formed two distinct clades. Two species clades for these genera are also observed in 16S rRNA gene trees and supported by average amino acid identity analysis. We also report here detailed analyses on protein sequences from Staphylococcaceae and Gemella genomes to identify conserved signature indels (CSIs) which are specific for different genus and family-level clades. These analyses have identified 120 novel CSIs robustly demarcating different proposed families and genera. The identified CSIs provide independent evidence that the genera Gemella, Jeotgalicoccus, Macrococcus and Salinicoccus consist of two distinct clades, which can be reliably distinguished based on multiple exclusively shared CSIs. We are proposing transfers of the species from the novel clades of the above four genera into the genera Gemelliphila gen. nov., Phocicoccus gen. nov., Macrococcoides gen. nov. and Lacicoccus gen. nov., respectively. The identified CSIs also provide strong evidence for division of Staphylococcaceae into an emended family Staphylococcaceae and two new families, Abyssicoccaceae fam. nov. and Salinicoccaceae fam. nov. All of these families can be reliably demarcated based on several exclusively shared CSIs.

Succession, Replacement, and Modification of Chicken Litter Microbiota

Chickens are in constant interaction with their environment, e.g., bedding and litter, and their microbiota. However, how litter microbiota develops over time and whether bedding and litter microbiota may affect the cecal microbiota is not clear. We addressed these questions using sequencing of V3/V4 variable region of 16S rRNA genes of cecal, bedding, and litter samples from broiler breeder chicken flocks for 4 months of production. Cecal, bedding, and litter samples were populated by microbiota of distinct composition. The microbiota in the bedding material did not expand in the litter. Similarly, major species from litter microbiota did not expand in the cecum. Only cecal microbiota was found in the litter forming approximately 20% of total litter microbiota. A time-dependent development of litter microbiota was observed. Escherichia coli, Staphylococcus saprophyticus, and Weissella jogaejeotgali were characteristic of fresh litter during the first month of production. Corynebacterium casei, Lactobacillus gasseri, and Lactobacillus salivarius dominated in a 2-month-old litter, Brevibacterium, Brachybacterium, and Sphingobacterium were characteristic for 3-month-old litter, and Salinococcus, Dietzia, Yaniella, and Staphylococcus lentus were common in a 4-month-old litter. Although the development was likely determined by physicochemical conditions in the litter, it might be interesting to test some of these species for active modification of litter to improve the chicken environment and welfare. IMPORTANCE Despite intimate contact, the composition of bedding, litter, and cecal microbiota differs considerably. Species characteristic for litter microbiota at different time points of chicken production were identified thus opening the possibility for active manipulation of litter microbiota.

Bacterial Communities in Concrete Reflect Its Composite Nature and Change with Weathering

Concrete is an extreme but common environment and is home to microbial communities adapted to alkaline, saline, and oligotrophic conditions. Microbes inside the concrete that makes up buildings or roads have received little attention despite their ubiquity and capacity to interact with the concrete. Because concrete is a composite of materials which have their own microbial communities, we hypothesized that the microbial communities of concrete reflect those of the concrete components and that these communities change as the concrete ages. Here, we used a 16S amplicon study to show how microbial communities change over 2 years of outdoor weathering in two sets of concrete cylinders, one prone to the concrete-degrading alkali-silica reaction (ASR) and the other having the risk of the ASR mitigated. After identifying and removing taxa that were likely laboratory or reagent contaminants, we found that precursor materials, particularly the large aggregate (gravel), were the probable source of ∼50 to 60% of the bacteria observed in the first cylinders from each series. Overall, community diversity decreased over 2 years, with temporarily increased diversity in warmer summer months. We found that most of the concrete microbiome was composed of Proteobacteria, Firmicutes, and Actinobacteria, although community composition changed seasonally and over multiyear time scales and was likely influenced by environmental deposition. Although the community composition between the two series was not significantly different overall, several taxa, including Arcobacter, Modestobacter, Salinicoccus, Rheinheimera, Lawsonella, and Bryobacter, appear to be associated with ASR.

IMPORTANCE Concrete is the most-used building material in the world and a biologically extreme environment, with a microbiome composed of bacteria that likely come from concrete precursor materials, aerosols, and environmental deposition. These microbes, though seeded from a variety of materials, are all subject to desiccation, heating, starvation, high salinity, and very high pH. Microbes that survive and even thrive under these conditions can potentially either degrade concrete or contribute to its repair. Thus, understanding which microbes survive in concrete, under what conditions, and for how long has potential implications for biorepair of concrete. Further, methodological pipelines for analyzing concrete microbial communities can be applied to concrete from a variety of structures or with different types of damage to identify bioindicator species that can be used for structural health monitoring and service life prediction.

From ecophysiology to cultivation methodology: filling the knowledge gap between uncultured and cultured microbes

Earth is dominated by a myriad of microbial communities, but the majority fails to grow under in situ laboratory conditions. The basic cause of unculturability is that bacteria dominantly occur as biofilms in natural environments. Earlier improvements in the culture techniques are mostly done by optimizing media components. However, with technological advancement particularly in the field of genome sequencing and cell imagining techniques, new tools have become available to understand the ecophysiology of microbial communities. Hence, it becomes easier to mimic environmental conditions in the culture plate. Other methods include co-culturing, emendation of growth factors, and cultivation after physical cell sorting. Most recently, techniques have been proposed for bacterial cultivation by employing genomic data to understand either microbial interactions (network-directed targeted bacterial isolation) or ecosystem engineering (reverse genomics). Hopefully, these techniques may be applied to almost all environmental samples, and help fill the gaps between the cultured and uncultured microbial communities.

Salinicoccus cyprini sp. nov., isolated from the gut of mirror carp, Cyprinus carpio var. specularis

A novel orange to pink coloured bacterial strain designated as CT19^T was isolated from the gastrointestinal tract of mirror carp, Cyprinus carpio var. specularis (Lacepède, 1803) collected from the Gobind Sagar reservoir at village Lathiani, Una, Himachal Pradesh, India. Cells of the strain were found to be aerobic, Gram-stain-positive, non-motile and non-spore-forming coccoids. Based on the 16S rRNA gene sequence, the strain was closely related to Salinicoccus hispanicus J-82^T (=DSM 5352^T; 97.4 %), followed by S. sesuvii CC-SPL15-2^T (=DSM 23267^T; 96.4 %), S. amylolyticus JC304^T (=KCTC 33661^T; 95.6 %) and S. roseus DSM 5351^T (95.4 %). Identity with all other members of the genus were <94.5 %. The draft genome of strain CT19^T was assembled to 2.4 Mbp with a G+C content of 47.9 mol%. Average nucleotide identity and digital DNA-DNA hybridization values between strain CT19^T and S. hispanicus J-82^T were found to be 85.9 and 31.3% respectively which is far below the threshold for species delineation. Iso-C_15 : 0, anteiso-C_15 : 0, iso-C_17 : 0, C_16 : 0 and anteiso-C_17 : 0 were the major cellular fatty acids of strain CT19^T. Major polar lipids were diphosphatidylglycerol, phosphatidylgylcerol and an unidentified glycolipid. Respiratory quinone system was composed of menaquinone-6 and major cell wall amino acid was l-lysine. Based on phylogenomic, physiological and biochemical characteristics, strain CT19^T represents a novel species of the genus Salinicoccus for which the name Salinicoccus cyprini sp. nov. is proposed. The type strain is CT19^T (=KCTC 43022^T =CCM 8886^T=MCC 3834^T).

Development of the first gene expression system for Salinicoccus strains with potential application in bioremediation of hypersaline wastewaters

Salinicoccus salsiraiae IM408 (=CGMCC13032) is a novel halophilic bacterium that we isolated from the saline soil of Da Gang Oilfield. It tolerates 60 g/l sodium chloride and up to 123 g/l (1.5 M) sodium acetate and has shown a potential application in bioremediation of wastewater with high salt and high chemical oxygen demand (COD). Two plasmids, pS408-1 and pS408-2, were identified in S. salsiraiae IM408, and the sequences and copy numbers of the plasmids were determined. Based on these plasmids, two shuttle vectors containing a replicon for Escherichia coli, ampicillin, and chloramphenicol resistance genes, as well as the replicon from pS408-1 or pS408-2, were constructed and named as pTCS101 and pTCS201, respectively. A suitable host strain, named S. salsiraiae PE01, was also developed from the wild-type by plasmid elimination. Using the plasmid pTCS101 as an expression vector, L-lactate dehydrogenase from Staphylococcus aureus was expressed successfully in S. salsiraiae PE01. This is the first gene expression system for the Salinicoccus genus. It has provided the potential for expression of desired proteins or for establishment of desired pathways in Salinicoccus strains, which would make these halophiles more advantageous in future biotechnological applications.

Salinicoccus amylolyticus sp. nov., isolated from a saltern

A Gram-stain-positive coccus, strain JC304T, was isolated from a saltern of Nari along the Bhavnagar Coast, Gujarat, India. The 16S rRNA gene sequence analysis and sequence comparison data indicated that JC304T represented a member of the genus Salinicoccus and was most closely related to Salinicoccus roseus 9T (99.6 %), Salinicoccus luteus YIM 70202T (97.0 %), Salinicoccus hispanicus J-82T (97.0 %) and the remaining species of the genus Salinicoccus (<97 %). Genome relatedness based on DNA-DNA hybridization of JC304T with the type strains of the most closely related species was less than 46 % and the ΔTmwas >5 °C indicating that the strain represents a novel species of the genus Salinicoccus. Independent and concatenated phylogenetic analysis of recA/fusA gene translated product showed a clear distinction of JC304T from its phylogenetic neighbors. Diphosphotidylglycerol, phosphatidylglycerol, an unidentified glycolipid and three unidentified lipids (L1, L2 and L3) were the polar lipids of JC304T. Iso-C15 : 0 and anteiso-C15 : 0 were the major (>10 %) fatty acids in strain JC304T. The cell-wall amino acids were l-lysine and d-glycine. Hopanoids were not detected. The major isoprenoid quinone was menaquinone (MK-6). The DNA G+C content of JC304T was 48 mol%. On the basis of physiological, genotypic, phylogenetic and chemotaxonomic analyses, strain JC304T is considered to represent a novel species of the genus Salinicoccus, for which the name Salinicoccusamylolyticus sp. nov. is proposed. The type strain is JC304T (=KCTC 33661T=LMG 28757T).

Haloparvum sedimenti gen. nov., sp. nov., a member of the family Haloferacaceae

Two extremely halophilic archaeal strains, DYS4T and Y2, were isolated from rock salt of the Jiangcheng Salt Mine, Yunnan province, China. Cells of the two strains were non-motile, pleomorphic rods and Gram-stain-negative. The cells produced light red-pigmented colonies. Strains DYS4T and Y2 required 2.6-3.4 M NaCl, pH 7.5- 8.0 and 42 ºC in aerobic conditions for optimal growth. Mg2+ was required for growth. The major polar lipids of both strains were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and sulfated mannosyl glucosyl diether. An unidentified minor glycolipid spot was present for strains DYS4T and Y2, which differentiates them from the closely related species of the genera Halorubrum and Halopenitus. The lipid core of the glycolipid was sn-2,3-diphytanylglycerol (C20C20). The sequence similarity of the 16S rRNA gene demonstrated that the closest relatives of strains DYS4T and Y2 were Halorubrum aidingense 31-hongT (94.1 % and 93.6 % 16S rRNA gene sequence similarity to DYS4T and Y2, respectively) and Halopenitus salinus SKJ47T (93.4% and 93.1%). Phylogenetic analysis of the 16S rRNA gene and the rpoB' gene revealed that strains DYS4T and Y2 formed an independent lineage closely related to the genera Halorubrum and Halopenitus. The DNA G+C contents of strains DYS4T and Y2 were 68.2 and 67.0 mol%, respectively. The DNA-DNA relatedness value between strains DYS4T and Y2 was 90.0 ± 0.5%, while that between strain DYS4T and other closest relatives was less than 26 % (19 ± 0.7 % for Halorubrum aidingense 31-hongT and 25 ± 0.3% for Halopenitus salinus SKJ47T). The phenotypic, chemotaxonomic and phylogenetic properties suggest that strains DYS4T and Y2 (=CGMCC 1.15000=JCM 30892) represent a novel species of a new genus within the family Haloferacaceae, for which the name Haloparvum sedimenti gen. nov., sp. nov. is proposed. The type strain of the type species is DYS4T (=CGMCC 1.14998T=JCM 30891T).

Genome sequence of the moderately halophilic bacterium Salinicoccus carnicancri type strain Crm(T) (= DSM 23852(T))

Salinicoccus carnicancri Jung et al. 2010 belongs to the genus Salinicoccus in the family Staphylococcaceae. Members of the Salinicoccus are moderately halophilic and originate from various salty environments. The halophilic features of the Salinicoccus suggest their possible uses in biotechnological applications, such as biodegradation and fermented food production. However, the genus Salinicoccus is poorly characterized at the genome level, despite its potential importance. This study presents the draft genome sequence of S. carnicancri strain Crm(T) and its annotation. The 2,673,309 base pair genome contained 2,700 protein-coding genes and 78 RNA genes with an average G+C content of 47.93 mol%. It was notable that the strain carried 72 predicted genes associated with osmoregulation, which suggests the presence of beneficial functions that facilitate growth in high-salt environments.

Diversity of Bacteria and Archaea in hypersaline sediment from Death Valley National Park, California

The objective of this study was to phylogenetically analyze microorganisms from the domains Bacteria and Archaea in hypersaline sediment from Death Valley National Park. Using domain-specific primers, a region of the 16S rRNA gene was amplified using polymerase chain reaction (PCR), and the product was subsequently used to create a clone library. A total of 243 bacterial clones, 99 archaeal clones, and 209 bacterial isolates were examined. The 243 clones from Bacteria were affiliated with the following groups: the Bacilli (59 clones) and Clostridia (1) of the Firmicutes, Bacteroidetes (90), Proteobacteria (27), Cyanobacteria (18), Gemmatimonadetes (41), candidate division OP1 (5), Actinobacteria (1), and the Deinococcus-Thermus division (1). Within the class Bacilli, 46 of 59 clones were tentatively identified as 10 unclassified species. The majority of bacterial isolates (130 of 209) were more closely related to the Bacillus subtilis–B. licheniformis clade than to any other recognized taxon, and an Ecotype Simulation analysis of B. subtilis relatives identified four previously unknown ecotypes. Several new genera were discovered within the Bacteroidetes (4) and the Gemmatimonadetes (2). Of the 99 archaeal clones, 94 were tentatively identified as belonging to 3 new genera within the Halobacteriaceae; other clones represented novel species within each of 4 established genera.

Salinicoccus sesuvii sp. nov., isolated from the rhizosphere of Sesuvium portulacastrum

A Gram-staining-positive coccus, designated CC-SPL15-2T, was isolated from the rhizosphere of Sesuvium portulacastrum. By 16S rRNA gene sequence analysis, it was shown that strain CC-SPL15-2T belonged to the genus Salinicoccus. The isolate was most closely related to Salinicoccus hispanicus DSM 5352T (98.3 % 16S rRNA gene sequence similarity) and Salinicoccus roseus DSM 5351T (96.7 %); similarities to all other members of the genus Salinicoccus were <96.5 %. In accordance with characteristics of the genus Salinicoccus, the quinone system was mainly composed of menaquinone MK-6. The polar lipid profile exhibited the major components diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. In the polyamine pattern, spermidine was the predominant compound. The fatty acids were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0, which supported the affiliation of strain CC-SPL15-2T to the genus Salinicoccus. DNA–DNA relatedness between strain CC-SPL15-2T and S. hispanicus CCUG 43288T was 42 and 32 % (reciprocal analysis). From these data as well as from physiological and biochemical tests, a clear differentiation of strain CC-SPL15-2T from S. hispanicus and other members of the genus Salinicoccus was possible. We propose that strain CC-SPL15-2T be assigned to a novel species, with the name Salinicoccus sesuvii sp. nov. The type strain is CC-SPL15-2T ( = DSM 23267T  = CCM 7756T).

Salinicoccus qingdaonensis sp. nov., isolated from coastal seawater during a bloom of green algae

A novel Gram-stain-positive, white-pigmented, non-motile, non-sporulating, catalase- and oxidase-positive, strictly aerobic coccus, designated strain ZXM223(T), was isolated from a seawater sample collected from the coast of Qingdao, PR China, during a green algal bloom. It grew at pH 6.0-10.5 and 0-25.0% (w/v) NaCl, with optimum growth at pH 8.5 and 3.0% (w/v) NaCl. Growth occurred at 16-42 °C (optimum at 28 °C). The major fatty acids were anteiso-C(15:0) and iso-C(15:0). Menaquinone 6 (MK-6) was the major respiratory quinone. The polar lipids were phosphatidylglycerol, three unidentified phospholipids and two unknown glycolipids. The peptidoglycan type was L-Lys-Gly(5-6.) The genomic DNA G+C content was 43.5 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed strain ZXM223(T) within the genus Salinicoccus, with sequence similarity of 92.2-97.1% between ZXM223(T) and the type strains of this genus. The closest relatives were Salinicoccus kunmingensis YIM Y15(T), 'S. salitudinis' YIM-C678 and S. alkaliphilus T8(T). The DNA-DNA relatedness between strain ZXM223(T) and S. kunmingensis CGMCC 1.6302(T) and 'S. salitudinis' CGMCC 1.6299 (=YIM-C678) was 37±3 and 30±2%, respectively. The phenotypic, chemotaxonomic and phylogenetic characteristics and low DNA-DNA relatedness support the proposal of a novel species of the genus Salinicoccus, Salinicoccus qingdaonensis sp. nov., with the type strain ZXM223(T) (=LMG 24855(T) =CGMCC 1.8895(T)).

Salinicoccus kekensis sp. nov., a novel alkaliphile and moderate halophile isolated from Keke Salt Lake in Qinghai, China

A novel alkaliphilic and moderate halophilic bacterium, designated strain K164(T), was isolated from Keke Salt Lake in Qinghai, China. The strain grew with 2.0-20.0% (w/v) NaCl, at 4-50 degrees C and pH 6.5-11.5, with an optimum of 8% (w/v) NaCl, 37degrees C and pH 10, respectively. The predominant respiratory quinone was menaquinone 6 (MK-6) and the major polar lipid was phosphatidylethanolamine. The major cellular fatty acids were anteiso-C(15:0) and iso-C(15:0). The genomic DNA G+C content was 50.16 mol. Phylogenetic analysis based on the full-length 16S rRNA gene sequence revealed that strain K164(T) was a member of the genus Salinicoccus. Strain K164(T) showed the highest similarity (98.4%) with Salinicoccus alkaliphilus AS 1.2691(T) and below 97% similarity with other recognized members of the genus in 16S rRNA gene sequence. Level of DNA-DNA relatedness between strain K164(T) and Salinicoccus alkaliphilus AS 1.2691(T) was 20.1%. On the basis of its phenotypic characteristics and the level of DNA-DNA hybridization, strain K164(T) is considered to represent a novel species of the genus Salinicoccus, for which the name Salinicoccus kekensis sp. nov. is proposed. The type strain is K164(T) (=CGMCC 1.10337(T) = DSM 23173(T)).

Salinicoccus carnicancri sp. nov., a halophilic bacterium isolated from a Korean fermented seafood

A novel, moderately halophilic bacterium belonging to the genus Salinicoccus was isolated from crabs preserved in soy sauce: a traditional Korean fermented seafood. Colonies of strain Crm(T) were ivory and the cells were non-motile, Gram-positive cocci. The organism was non-sporulating, catalase-positive and oxidase-negative. The major fatty acids of strain Crm(T) were iso-C(15 : 0) (22.0 %), anteiso-C(15 : 0) (40.6 %) and anteiso-C(17 : 0) (12.1 %). The cell wall peptidoglycan contained lysine and glycine, and the major isoprenoid quinone was MK-6. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid. The genomic DNA G+C content was 47.8 mol%. Strain Crm(T) was closely related to the type strain of Salinicoccus halodurans, with which it shared 96.9 % 16S rRNA gene sequence similarity. The DNA-DNA hybridization value between strains Crm(T) and S. halodurans DSM 19336(T) was 7.6 %. Based on phenotypic, genetic and phylogenetic data, strain Crm(T) should be classified as a novel species within the genus Salinicoccus , for which the name Salinicoccus carnicancri sp. nov. is proposed. The type strain is Crm(T) (=KCTC 13301(T) =JCM 15796(T)).