Limibaculum halophilum gen. nov., sp. nov., a new member of the family Rhodobacteraceae

Shin, Yong Ho; Kim, Jong-Hwa; Suckhoom, Ampaitip; Kantachote, Duangporn; Kim, Wonyong

doi:10.1099/ijsem.0.002200

Cited by 17 publications

(5 citation statements)

References 42 publications

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“…Other OTUs are related to Limibaculum (“uncultured 6” and “uncultured 7”) and Rhodothalassium (“uncultured 66”) and were detected in surface sediments of the Nueces River mouth and the Gulf of Mexico. L. halophilum has been shown to be aerobic, hydrolyzing gelatin, using some sugars and also more complex substrates, e.g., potassium 5-ketogluconate (Shin et al, 2017). The isolate of the genus Rhodothalassium has grown preferably photoorganotrophically under anoxic conditions in the light, but can also thrive under microoxic to oxic conditions in the dark (Drews, 1981; Imhoff et al, 1998).…”

Section: Discussionmentioning

confidence: 99%

The Majority of Active Rhodobacteraceae in Marine Sediments Belong to Uncultured Genera: A Molecular Approach to Link Their Distribution to Environmental Conditions

et al. 2019

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General studies on benthic microbial communities focus on fundamental biogeochemical processes or the most abundant constituents. Thereby, minor fractions such as the Rhodobacteraceae are frequently neglected. Even though this family belongs to the most widely distributed bacteria in the marine environment, their proportion on benthic microbial communities is usually within or below the single digit range. Thus, knowledge on these community members is limited, even though their absolute numbers might exceed those from the pelagic zone by orders of magnitudes. To unravel the distribution and diversity of benthic, metabolically active Rhodobacteraceae , we have now analyzed an already existing library of bacterial 16S rRNA transcripts. The dataset originated from 154 individual sediment samples comprising seven oceanic regions and a broad variety of environmental conditions. Across all samples, a total of 0.7% of all 16S rRNA transcripts was annotated as Rhodobacteraceae. Among those, Sulfitobacter , Paracoccus , and Phaeomarinomonas were the most abundant cultured representatives, but the majority (78%) was affiliated to uncultured family members. To define them, the 45 most abundant Rhodobacteraceae -OTUs assigned as “uncultured” were phylogenetically assembled in new clusters. Their next relatives particularly belonged to different subgroups other than the Roseobacter group, reflecting a large part of the hidden diversity within the benthic Rhodobacteraceae with unknown functions. The general composition of active Rhodobacteraceae communities was found to be specific for the geographical location, exhibiting a decreasing richness with sediment depth. One-third of the Rhodobacteraceae -OTUs significantly responded to the prevailing redox regime, suggesting an adaption to anoxic conditions. A possible approach to predict their physiological properties is to identify the metabolic capabilities of their nearest relatives. Those need to be proven by physiological experiments, as soon an isolate is available. Because many uncultured members of these subgroups likely thrive under anoxic conditions, in future research, a molecular-guided cultivation strategy can be pursued to isolate novel Rhodobacteraceae from sediments.

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Section: Discussionmentioning

confidence: 99%

The Majority of Active Rhodobacteraceae in Marine Sediments Belong to Uncultured Genera: A Molecular Approach to Link Their Distribution to Environmental Conditions

et al. 2019

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“…(Sharma et al, 2015;Van Gerrewey et al, 2021;Vives-Peris et al, 2018) responded to treatments further supporting this observation. Nevertheless, four taxa which exhibited higher abundances in the urine treatments, could shelter moderately halotolerant species: Sneathiella (marine bacteria) (Austin, 2014) Limibaculum halophilum (2 % NaCl) (Shin et al, 2017), Lysobacter aestuarii (0-7 % NaCl) (Jeong et al, 2016) and Mesorhizobium (0-3 % NaCl) (Laranjo and Oliveira, 2011). These findings suggest that urine salt content may selectively favour a small number of halotolerant bacteria without impeding the survival of nonhalotolerant bacteria.…”

Section: Effects Of Urine On Nutrient Cycling and Bacteria Involved I...mentioning

confidence: 90%

Unveiling the Impact of Human Urine Fertilization on Soil Bacterial Communities: A Path Toward Sustainable Fertilization

Rumeau,

Pistocchi,

Ait-Mouheb

et al. 2024

Preprint

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“…Talassobius, a strictly aerobic, chemo-organotrophic bacterium [35], can reduce nitrate to nitrite [36]. Limibaculum [37] and Rubellimicrobium [38] are important denitrifying bacteria. HIMB11 can utilise ammonia, as well as inorganic and organic forms of phosphorus [39].…”

Section: Discussionmentioning

confidence: 99%

Bivalves Improved Water Quality by Changing Bacterial Composition in Sediment and Water in an IMTA System

Kong

Chen

Ghonimy

et al. 2023

Aquaculture Research

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Integrated multitrophic aquaculture (IMTA) maximises the nitrogen cycle between system components, including bacteria. In order to maximise the bacterial role in nitrogen elimination in an IMTA system, we investigated the effect of bivalve culture on water quality and bacterial community structure in overlying water and sediment in the “shrimp-crab-bivalve-fish” IMTA system. The bacterial composition in overlying water and sediment was measured by Illumina -MiSeq high-throughput sequencing technology. The results show that dissolved oxygen was higher in the bivalve culture area. Ammonia and nitrite in the bivalve culture area were lower than those in the nonbivalve culture area; however, the nitrate and phosphate in the bivalve culture area were higher than those in the nonbivalve culture area. The Chao1, Shannon, and Ace indexes were higher in the bivalve area. More bacteria with nitrification and denitrification functions were detected in bivalve culture areas, such as Ruegeria (1.05%–4.79%), Thalassobius (0.11%–0.69%), Limibaculum (0.07%–0.69%), HIMB11 (0.13%–0.21%), and Rubellimicrobium (0.01%–0.16%). More Cyanobacteria were detected in bivalve culture areas with higher phosphate concentrations. To sum up, bivalves can release phosphorus through bioturbation, increasing the abundance of Cyanobacteria, which release dissolved oxygen into overlying water through photosynthesis, enhance nitrification (mainly ammonia oxidation), and improve the ammonia nitrogen removal capacity of the system. Meanwhile, bivalves can increase bacterial diversity and abundance by regulating dissolved oxygen. This study provided insight into bivalve interaction with bacterial activity in the IMTA system.

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Limibaculum halophilum gen. nov., sp. nov., a new member of the family Rhodobacteraceae

Cited by 17 publications

References 42 publications

The Majority of Active Rhodobacteraceae in Marine Sediments Belong to Uncultured Genera: A Molecular Approach to Link Their Distribution to Environmental Conditions

The Majority of Active Rhodobacteraceae in Marine Sediments Belong to Uncultured Genera: A Molecular Approach to Link Their Distribution to Environmental Conditions

Unveiling the Impact of Human Urine Fertilization on Soil Bacterial Communities: A Path Toward Sustainable Fertilization

Bivalves Improved Water Quality by Changing Bacterial Composition in Sediment and Water in an IMTA System

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