Diversity of nitrifying bacteria in microbial communities from water and epilithic biofilms of the Lake Baikal littoral zone

Podlesnaya, G. V.; Krasnopeev, Andrey; Potapov, Sergey; Тихонова, И. В.; Shtykova, Yu. R.; Suslova, M. Yu.; Тимошкин, О. А.; Белых, О. И.

doi:10.31951/2658-3518-2020-a-4-1008

Cited by 8 publications

(6 citation statements)

References 9 publications

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“…Additionally, combined with the results from functional prediction, genes involved in denitrification were abundant in DO sufficient sites. Ellin6067 had been reported as a group of significant ammonia oxidizing bacteria (Podlesnaya et al, 2020) and could be inhibited by activity when DO content was low (Huang et al, 2018). The only occurrence of both Amphiplicatus and Ellin6067 in August in our study indicated that oxygen might not be a limiting factor but could be an indicator for their distribution in marine environment.…”

Section: Switch Of Bacteria Community In Response To Oxygen Depletionmentioning

confidence: 49%

Switch of Bacteria Community Under Oxygen Depletion in Sediment of Bohai Sea

Guo

Song

et al. 2022

Front. Mar. Sci.

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Regular oxygen depletion is occurring every summer in the depression area of the Bohai Sea. The community structure and potential functions of microbes in expanding marine hypoxic area are of great importance due to their roles in biogeochemical cycling. In this study, the diversity and distribution of bacteria based on 16S rRNA gene in sediment along an inshore-offshore transect across the oxygen-depletion area in the Bohai Sea was investigated in June, July and August of 2018 by employing high-throughput sequencing. Results revealed that the bacteria community was dominated by Proteobacteria (42.67%), Actinobacteria (14.13%), Chloroflexi (13.02%), Acidobacteria (8.01%), and Bacteroidetes (6.30%). During oxygen depletion, the bacteria community from inshore site A3 subjected to dramatic variation from June to August, but the composition tended to be stable in sites from the depression area along the transect. Distinct switch of bacteria from aerobic to anaerobic group was observed when the DO concentration <4.2 mg/L, typically represented by dominance of Anaerolineaceae in August sample. Further, KEGG prediction by PICRUSt confirmed the variations by showing significant difference in functional pathways, especially the nitrogen metabolisms, before and after DO depletion (p < 0.05). These variations could be influenced by depth, NO2– concentration and DO availability based on RDA analysis. The details in diversity and composition of bacteria under continually observation provide insights into both instant and long-term response of bacteria community to oxygen depletion, and the distinct functional switch under this process expands our knowledge on the metabolic character of bacteria in worldwide hypoxia areas.

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Section: Switch Of Bacteria Community In Response To Oxygen Depletionmentioning

confidence: 49%

Switch of Bacteria Community Under Oxygen Depletion in Sediment of Bohai Sea

Guo

Song

et al. 2022

Front. Mar. Sci.

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“…N 2 O is released by bacteria due to incomplete denitrification (Palta et al., 2013), an anaerobic process that is primarily reliant on the generation of nitrate from nitrification by ammonia‐oxidizing bacteria (AOB) and/or archaea (AOA) (Beeckman et al., 2018). High relative abundances of Nitrosomonadaceae (Burkholderiales Order; Figure 3), a family of Burkholderiales containing species capable of ammonia oxidation (Podlesnaya et al., 2020), were found across sample sites, especially the beaver ponds. Though weakly based on 16S rRNA gene identity, this could indicate a higher prevalence of ammonia oxidation in beaver ponds than in other sample sites, which could provide substrate for denitrification.…”

Section: Discussionmentioning

confidence: 99%

Comparing Sediment Microbial Communities of Arctic Beaver Ponds to Tundra Lakes and Streams

et al. 2023

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In recent decades the habitat of North American beaver (Castor canadensis) has expanded from boreal forests into Arctic tundra ecosystems. Beaver ponds in Arctic watersheds are known to alter stream biogeochemistry, which is likely coupled with changes in the activity and composition of microbial communities inhabiting beaver pond sediments. We investigated bacterial, archaeal, and fungal communities in beaver pond sediments along tundra streams in northwestern Alaska (AK), USA and compared them to those of tundra lakes and streams in north‐central Alaska that are unimpacted by beavers. β‐glucosidase activity assays indicated higher cellulose degradation potential in beaver ponds than in unimpacted streams and lakes within a watershed absent of beavers. Beta diversity analyses showed that dominant lineages of bacteria and archaea in beaver ponds differed from those in tundra lakes and streams, but dominant fungal lineages did not differ between these sample types. Beaver pond sediments displayed lower relative abundances of Crenarchaeota and Euryarchaeota archaea and of bacteria from typically anaerobic taxonomic groups, suggesting differences in rates of fermentative organic matter (OM) breakdown, syntrophy, and methane generation. Beaver ponds also displayed low relative abundances of Chytridiomycota (putative non‐symbiotic) fungi and high relative abundances of ectomycorrhizal (plant symbionts) Basidiomycota fungi, suggesting differences in the occurrence of plant and fungi mutualistic interactions. Beaver ponds also featured microbes with taxonomic identities typically associated with the cycling of nitrogen and sulfur compounds in higher relative abundances than tundra lakes and streams. These findings help clarify the microbiological implications of beavers expanding into high latitude regions.

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“…As Sphingomonas was seen to be abundant in CF-treated soils, this could be the reason for frequent BLB cases faced by Indonesian local farmers. The SF-treated soils were seen to be abundant in MND1, an ammonia-oxidizing bacteria (AOB) [55,56], particularly CFSF1, which shows significant abundance compared to CFSF2 and SF.…”

Section: Taxonomic Abundance Cluster Heatmapmentioning

confidence: 99%

Seaweed Fertilizer Prepared by EM-Fermentation Increases Abundance of Beneficial Soil Microbiome in Paddy (Oryzasativa L.) during Vegetative Stage

et al. 2022

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Excessive use of chemical fertilizer could potentially decrease soil productivity by decreasing soil microbiome diversity. In this study, we evaluated the effects of fermented seaweed fertilizer in the soil microbial community of paddy plants (Oryza sativa L.). The paddy seedlings were divided into five groups, control (C0), chemical fertilizer (CF), seaweed fertilizer (SF), chemical and seaweed fertilizer combination 50:50 (CFSF1), and chemical and fertilizer combination 75:25 (CFSF2). The CFSF1 combination showed to be the most effective in inducing plant height (83.99 ± 3.70 cm) and number of tillers (24.20 ± 4.08). After 8 weeks after transplantation, the isolated DNA from each soil treatment were subjected to 16S rRNA (v3–v4 region) next-generation sequencing. The beneficial Acidobacteriota was most abundant in CFSF1. At genus level, the nitrifying bacteria MND1 was seen to be abundant in CFSF1 and also present in other SF treatments. The genus Chujaibacter is highly abundant in CF, which potentially plays a role in denitrification resulting in soil degradation. In addition, the CFSF1-treated soils show significantly higher diversity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). The current results could potentially contribute to the utilization of SF as a bioremediator and promoting green agriculture practice by reducing the amount of CF usage.

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Diversity of nitrifying bacteria in microbial communities from water and epilithic biofilms of the Lake Baikal littoral zone

Cited by 8 publications

References 9 publications

Switch of Bacteria Community Under Oxygen Depletion in Sediment of Bohai Sea

Switch of Bacteria Community Under Oxygen Depletion in Sediment of Bohai Sea

Comparing Sediment Microbial Communities of Arctic Beaver Ponds to Tundra Lakes and Streams

Seaweed Fertilizer Prepared by EM-Fermentation Increases Abundance of Beneficial Soil Microbiome in Paddy (Oryzasativa L.) during Vegetative Stage

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