Prokaryotic Communities Research Articles

Study on the treatment of corn alcohol wastewater by the internal circulation anaerobic reactor.

To comprehensively assess the efficacy of employing the internal circulation (IC) anaerobic reactor for corn alcohol wastewater treatment and investigate its feasibility, this study focused on anaerobic digestion parameters, energy balance, and the composition of the prokaryotic microbial community. During the operation of the reactor, the hydraulic retention time was progressively reduced from 4.8 to 1.6 days while achieving an average organic loading rate of 12.46 kg chemical oxygen demand (COD)/(m3·d). Moreover, the removal rate of COD exceeded 98%, and the energy balance (ΔE) reached 10.29 kJ/g fed COD. The initial manifestation of organic acidosis in the reactor was a decline in gas production, which is primarily caused by propionic acid accumulation. The subsequent analysis revealed a high diversity of prokaryotes in granular sludge, with the predominant archaea primarily involved in methane production through the acetic acid pathway. The IC anaerobic reactor shows exceptional performance in treating corn alcohol wastewater by optimizing its operating conditions. Energy balance analysis confirmed the feasibility of the process. The findings of this study may offer valuable insights for optimizing control strategies and engineering applications.

Salinity-controlled distribution of prokaryotic communities in the Arctic sea-ice melt ponds.

The thawing of snow and sea ice produces distinctive melt ponds on the surface of the Arctic sea ice, which covers a significant portion of the surface sea ice during summer. Melt-pond salinity impacts heat transfer to the ice below and the melting rate. It is widely known that melt ponds play a significant role in heat fluxes, ice-albedo feedback, and sea-ice energy balance. However, not much attention has been given to the fact that melt ponds also serve as a unique microbial ecosystem where microbial production begins as soon as they are formed. Here, we investigated the role of melt pond salinity in controlling the diversity and distribution of prokaryotic communities using culture-dependent and -independent approaches. The 16S rRNA gene amplicon based next generation sequencing analysis retrieved a total of 14 bacterial phyla, consisting of 146 genera, in addition to two archaeal phyla. Further, the culture-dependent approaches of the study allowed for the isolation and identification of twenty-four bacterial genera in pure culture. Flavobacterium, Candidatus_Aquiluna, SAR11 clade, Polaribacter, Glaciecola, and Nonlabens were the dominant genera observed in the amplicon analysis. Whereas Actimicrobium, Rhodoglobus, Flavobacterium, and Pseudomonas were dominated in the culturable fraction. Our results also demonstrated that salinity, chlorophyll a, and dissolved organic carbon were the significant environmental variables controlling the prokaryotic community distribution in melt ponds. A significant community shift was observed in melt ponds when the salinity changed with the progression of melting and deepening of ponds. Different communities were found to be dominant in melt ponds with different salinity ranges. It was also observed that melt pond prokaryotic communities significantly differed from the surface ocean microbial community. Our observations suggest that complex prokaryotic communities develop in melt ponds immediately after its formation using dissolved organic carbon generated through primary production in the oligotrophic water.

Microbial perspective of inhibited carbon turnover in Tangel humus of the Northern Limestone Alps.

Tangel humus primarily occurs in montane and subalpine zones of the calcareous Alps that exhibit low temperatures and high precipitation sums. This humus form is characterized by inhibited carbon turnover and accumulated organic matter, leading to the typical thick organic layers. However, the reason for this accumulation of organic matter is still unclear, and knowledge about the microbial community within Tangel humus is lacking. Therefore, we investigated the prokaryotic and fungal communities along with the physical and chemical properties within a depth gradient (0-10, 10-20, 20-30, 30-40, 40-50 cm) of a Tangel humus located in the Northern Limestone Alps. We hypothesized that humus properties and microbial activity, biomass, and diversity differ along the depth gradient and that microbial key players refer to certain humus depths. Our results give the first comprehensive information about microbiota within the Tangel humus and establish a microbial zonation of the humus. Microbial activity, biomass, as well as microbial alpha diversity significantly decreased with increasing depths. We identified microbial biomarkers for both, the top and the deepest depth, indicating different, microbial habitats. The microbial characterization together with the established nutrient deficiencies in the deeper depths might explain reduced C-turnover and Tangel humus formation.

Contrasting resistance of prokaryotic plankton biomass and community composition to experimental nutrient inputs in a coastal upwelling system (NW Spain)

Contrasting resistance of prokaryotic plankton biomass and community composition to experimental nutrient inputs in a coastal upwelling system (NW Spain)

Elucidating potential bioindicators from insights in the diversity and assembly processes of prokaryotic and eukaryotic communities in the Mekong River

Drivers for spatio-temporal distribution patterns of overall planktonic prokaryotes and eukaryotes in riverine ecosystems are generally not fully understood. This study employed amplicon metabarcoding to investigate the distributions and assembly mechanisms of bacterial and eukaryotic communities in the Mekong River. The prevailing bacteria taxa were found to be Betaproteobacteria, Actinobacteria, and Bacteroidetes, while the dominant eukaryotic organisms were cryptophytes, chlorophytes, and diatoms. The community assemblages were influenced by a combination of stochastic and deterministic processes. Drift (DR) and dispersal limitation (DL), signifying the stochastic mechanism, were the main processes shaping the overall prokaryotic and eukaryotic communities. However, homogeneous selection (HoS), indicating deterministic mechanism, played a major role in the assembly process of core prokaryotic communities, especially in the wet season. In contrast, the core eukaryotic communities including Opisthokonta, Sar, and Chlorophyta were dominated by stochastic processes. The significance of HoS within prokaryotic communities was also found to exhibit a decreasing trend from the upstream sampling sites (Chiang Saen and Chiang Khan, Nong Khai) towards the downstream sites (Mukdahan, and Khong Chiam) of the Mekong River. The environmental gradients resulting from the site-specific variations and the gradual decrease in elevation along the river may have a potential influence on the role of HoS in community assembly. Crucial environmental factors that shape the phylogenetic structure within distinct bins of the core prokaryotic communities including water depth, temperature, chloride, sodium, and sulphate were identified, as inferred by their correlation with the beta Net Relatedness Index (betaNRI) during the wet season. Overall, these findings enhance understanding of the complex mechanisms governing the spatio-temporal dynamics of prokaryotic and eukaryotic communities in the Mekong River. Finally, insights gained from this study could provide information on further use of specific core bacteria as microbial-based bioindicators that are effective for the assessment and conservation of the Mekong River ecosystem.

Contrasting drivers of abundant phage and prokaryotic communities revealed in diverse coastal ecosystems

Phages (viruses of bacteria and archaea) are a ubiquitous top-down control on microbial communities by selectively infecting and killing cells. As obligate parasites, phages are inherently linked to processes that impact their hosts’ distribution and physiology, but phages can also be impacted by external, environmental factors, such as UV radiation degrading their virions. To better understand these complex links of phages to their hosts and the environment, we leverage the unique ecological context of the Isthmus of Panama, which narrowly disconnects the productive Tropical Eastern Pacific (EP) and nutrient-poor Tropical Western Atlantic (WA) provinces. We could thus compare patterns of phage and prokaryotic communities at both global scales (between oceans) and local-scales (between habitats within an ocean). Although both phage and prokaryotic communities differed sharply between the oceans, phage community composition did not significantly differ between mangroves and reefs of the WA, while prokaryotic communities were distinct. These results suggest phages are more shaped by dispersal processes than local conditions regardless of spatial scale, while prokaryotes tend to be shaped by local conditions at smaller spatial scales. Collectively, we provide a framework for addressing the co-variability between phages and prokaryotes in marine systems and identifying factors that drive consistent versus disparate trends in community shifts, essential to informing models of biogeochemical cycles that include these interactions.

Carbon and Nutrients from Organic Residues Modulate the Dynamics of Prokaryotic and Fungal Communities.

Inputs of carbon (C) and nutrients from organic residues may select specific microbes and shape the soil microbial community. However, little is known about the abiotic filtering of the same residues with different nutrient concentrations applied to the soil. In our study, we explored how applying organic residue, vinasse, as fertilizer in its natural state (V) versus its concentrated form (CV) impacts soil microbiota. We conducted two field experiments, evaluating soil prokaryotic and fungal communities over 24 and 45 days with vinasse (V or CV) plus N fertilizer. We used 16S rRNA gene and ITS amplicon sequencing. Inorganic N had no significant impact on bacterial and fungal diversity compared to the control. However, the varying concentrations of organic C and nutrients in vinasse significantly influenced the soil microbiome structure, with smaller effects observed for V compared to CV. Prokaryotic and fungal communities were not correlated (co-inertia: RV coefficient = 0.1517, p = 0.9708). Vinasse did not change the total bacterial but increased the total fungal abundance. A higher C input enhanced the prokaryotic but reduced the fungal diversity. Our findings highlight vinasse's role as an abiotic filter shaping soil microbial communities, with distinct effects on prokaryotic and fungal communities. Vinasse primarily selects fast-growing microorganisms, shedding light on the intricate dynamics between organic residues, nutrient concentrations, and soil microbes.

Changes in the structure and function of soil prokaryotic communities in subalpine Picea asperata plantations

The structural and functional characteristics of soil prokaryotic community are important for maintaining ecosystem functions. In this study, we examined the diversity and compositions, the key drivers, as well as functional characteristics of prokaryotic communities in the rhizosphere and non-rhizosphere soils of Picea asperata with different stand ages using high-throughput sequencing technique and bioinformatics methods. The results showed that β-diversity of soil prokaryotic communities in both rhizosphere and non-rhizosphere showed significant differences among different stand ages, but no significant difference between rhizosphere and non-rhizosphere in the same stand age. In terms of community composition at the phylum level, the relative abundances of Proteobacteria and Rokubacteria showed an increasing trend with the increases of stand age, while the relative abundance of Actinobacteria showed a decreasing trend, but no significant difference was observed between 75 year-old planted forests (PF75) and natural forests (NF). The relative abundances of Firmicutes and Thaumarchaeota in the soil of the 25 year-old planted forests (PF25) were significantly higher than in other planted forests and NF. At the genus level, the relative abundances of RB41, Terrimonas and Acidibacter showed an increasing trend with the increases of stand age, and RB41 and Terrimonas in rhizosphere soil of PF75 were significantly higher than those in NF. Soil properties and vegetation characteristics jointly influenced the structure of soil prokaryotic communities, with herb layer coverage, soil pH, total phosphorus, and total nitrogen as major drivers. The functional characteristics of soil prokaryotic communities were significantly different among different stand ages. The relative abundances of functions involved in carbon and nitrogen cycle, e.g., cellulolysis and nitrification, decreased with the increases of stand age, whereas that of sulfate respiration involved in the sulfur cycle increased. We proposed that the structure and functional characteristics of soil prokaryotic communities could serve as important indicators of the development stages of P. asperata forests. In the later stages of plantation forest development, soil nutrient availability could be improved by mediating phosphorus-dissolving and nitrogen-enhancing microorganisms to maintain the stability of the plantation ecosystem.

Antibacterial, antifungal and antioxidant activities of Bacillus cereus SMPRL-2 isolated from seaweeds Eucheuma cottonii

Seaweeds have a strong relationship with prokaryotic community especially bacteria. Bacteria-associated with seaweeds generally produce active compounds which could be potential for pharmaceutical purposes. This research was focused to study antibacterial, antifungal and antioxidant activities from a bacteria encoded as SMPRL-2, isolated from Eucheuma cottonii. Molecular identification of the isolate was performed based on 16S rRNA sequencing and its morphology was assessed using scanning electronic microscope (SEM). The isolate SMPRL-2 was fermented in 100 mL ISP-2 liquid media for 14 days and extracted using ethyl acetate (1:1 ratio, v/v). The obtained crude extract was screened against bacterial and fungal isolates based on Kirby-Bauer method. The extract was screened for its antioxidant activities using DPPH method. The isolate was identified as Bacillus cereus, with short rod morphology under SEM observation. Zone of inhibition (ZOI) of the extract was 14.7±0.8 mm and 9.1±0.8 mm against Streptococcus mutans FNCC 0405 and Escherichia coli ATCC 25922, respectively. Furthermore, ZOI of the extract against Candida albicans and Aspergillus flavus were 9.6±0.9 mm and 8.8±2.3 mm respectively. A very weak antioxidant activity with IC50 value of 33000 ppm was observed. Overall, this result provides a preliminary finding of marine bacteria as naturally active compounds producer.

Heterogeneous Diazotroph Communities in the Subtropical‐Subantarctic Transition and Aphotic Zones Off the Coast of Patagonia, Eastern South Pacific Ocean

AbstractSubtropical‐subpolar transition water is a potential domain for N2 fixation, but the understanding of N2 fixation in such waters remains incomplete. We simultaneously examined the N2 fixation activity and community structures of diazotrophs and all prokaryotes from the surface to just above the seafloor off Patagonia in the transitional region of the eastern South Pacific Ocean. N2 fixation activity was not detected in the surface waters, but was observed sporadically and only in subpolar bathypelagic waters (>1,000 m) at very low rates (0.02–0.06 nmol N L−1 d−1). By contrast, the nifH gene, a key gene involved in N2 fixation, was detected widely from the surface to the bottom waters. The majority of diazotrophs were classified as non‐cyanobacterial diazotrophs (NCDs), and the nifH amino acid sequences of major diazotrophs were similar to sequences detected in the Southern Ocean, the aphotic zone and sediment of other oceans, and estuarine waters, suggesting that the NCDs are distributed across diverse marine environments. The overall prokaryotic communities were generally similar to those in other open ocean regions at the phylum level (class level for Proteobacteria) and differed among water depths. Diazotrophs, in contrast, showed vertical and horizontal heterogeneity below the euphotic zone and little association with water depth, indicating a lack of cohesion within the community, which may characterize diazotroph community in the transitional surface water and aphotic zones. Elucidating this community heterogeneity may provide pivotal information about N2 fixation in these waters.

Synthetic Communities Increase Microbial Diversity and Productivity of Agave tequilana Plants in the Field

Agaves are plants native to North America that sustain life in arid and semiarid ecosystems. Previous studies revealed that cultivated plants of Agave tequilana had lower microbial diversity and functionality than wild Agave species. Here, we tested if synthetic communities (syncoms), based on microbial hubs or taxa with enriched microbial functions, could increase microbial diversity, plant health, and productivity in A. tequilana. We applied 10 syncoms to the phyllospheres of 6-month-old plants of A. tequilana in the field and monitored their development for 2 years. Amplicon sequencing of 16S-rRNA-V4 and ITS2 revealed that the inoculated syncoms played a negligible or minor role in the assembly of the prokaryotic and eukaryotic phyllospheric communities associated with A. tequilana, respectively. However, syncoms based on microbial hubs, particularly those observed in the phyllosphere associated with wild A. salmiana (PFCS), promoted microbial communities with higher alpha diversity. Some of these syncom-derived phyllospheric communities consumed a greater variety of carbon sources; had more complex co-occurrence networks; and increased the content of sugars (oBrix, a measure of productivity in agaves) in the stem and changed the leaf metabolome. Our work demonstrates that the application of syncoms formulated based on predicted microbe–microbe interactions and metagenomic analyses of microbial communities in cultivated and wild plant species represents an effective tool to improve the sustainability and productivity of crops in arid ecosystems. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Abstract C135: The oral microbiome and short chain fatty acids as contributors to oral HPV disparities in Puerto Rican people with HIV

Abstract Human papillomavirus (HPV) is the most common malignancy worldwide, accounting for more than 70% of oropharyngeal cancers. People living with HIV (PWH) are disproportionately affected by HPV infection and are at higher risk of HPV-associated oral complications, dysplasia, and cancer, even with suppressive antiretroviral therapy (ART), suggesting that ART may not fully recover oral HPV-specific immunity. Particularly, Puerto Rico (PR) has a significant burden and disparity for both HIV and HPV infections and related cancers. Dysbiosis of the oral microbiome occurs in PWH, characterized by a decrease in diversity, and a change in the abundance of microbial products important for human health and disease. The relationship of the oral microbiome with HPV infection is poorly understood, particularly in PWH. In this study, we measured oral microbial diversity and products, such as short chain fatty acids (SCFA), in saliva and evaluated them in the context of HPV infection in PWH. We evaluated 48 sexually active PWH (17 HPV+ and 31 HPV-) from a community clinic in San Juan, Puerto Rico. Oral rinse samples were collected and analyzed for HPV infection and genotyped using the DNA ELISA kit HPV SPF10 and RHA kit HPV SPF10-LiPA25 which detects 40 HPV subtypes. We characterized oral prokaryotic communities by sequencing 16S rDNA and quantified the levels of SCFAs (acetate, propionate, iso-butyrate, butyrate, iso-valerate, valerate, and hexanoate) in saliva using GC-MS. Statistical analyses of bacterial diversity and levels of SCFA were assessed in relation to HPV status using R-statistical software. PWH had a median CD4 count of 738 cells/µL [IQR: 649-887]. PWH with HPV had a 73% (11/15) of high-risk HPV genotypes, with HPV-18 being the most prevalent subtype (6/17). While there was no significant difference in alpha diversity (Shannon: p=0.23 and Observed features: p=0.28), bacterial communities were clustered according to HPV status using a Bray-Curtis dissimilarity index. Furthermore, PWH with HPV showed higher levels of butyrate (p=0.07) and significantly lower levels of hexanoate (p=0.05) in saliva. Particularly, PWH with the HPV-18 subtype had lower levels of hexanoate than other HPV subtypes and HPV- PWH (p=0.03). Overall, these findings suggest that the oral microbiome and SCFA are associated with HPV infection and the presence of specific HPV subtypes. While a difference in bacterial diversity might not be driving HPV infection, different bacterial groupings might affect the abundance of specific SCFA, such as butyrate, which can contribute to local inflammation and periodontal tissue damage, providing an ideal environment for HPV infection and persistence. Understanding how the oral microbiota could facilitate HPV infection and other comorbidities in PWH is crucial for the development of cancer prevention and reduce the burden of HPV-associated malignancies in PWH. Furthermore, HPV vaccine-oriented and oral health educational interventions should target this high-risk group. Citation Format: Yabdiel A. Ramos Valerio, Eduardo S. Perez Delgado, Maria M. Sanchez, Ramon F. Gonzalez Garcia, Ana P. Ortiz Martinez, Magaly Martinez Ferrer, Josue Perez Santiago. The oral microbiome and short chain fatty acids as contributors to oral HPV disparities in Puerto Rican people with HIV [abstract]. In: Proceedings of the 16th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2023 Sep 29-Oct 2;Orlando, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2023;32(12 Suppl):Abstract nr C135.

Stratification of Prokaryotic Communities in the White Sea Bottom Sediments

Stratification of Prokaryotic Communities in the White Sea Bottom Sediments

Effect of dietary phytase on water and fecal prokaryotic and eukaryotic microbiomes in a hybrid tilapia (Oreochromis aureus x O. niloticus) mixotrophic biofloc production system

In this study we evaluated feed and temporal effects on prokaryotic (16S) and eukaryotic (18S) microbiome dynamics in an outdoor mixotrophic biofloc system used to grow hybrid tilapia (Oreochromis aureus x O. niloticus) to market size. The dicalcium phosphate -free practical feed treated with 6-phytase (3000 FTU/kg; P-Free+Phytase) and positive (Control) and negative (P-Free) control practical feeds used were formulated to contain 27.7% digestible protein and 4% lipid. Sex reversed, all-male hybrid tilapia (28.9 g/fish) were stocked (29 fish/m3) in 9 outdoor rectangular tanks (16.6 m3) and grown for 154 days. The Control feed was fed to all fish during the 14-day acclimation period after which each test feed was fed to fish in three tanks/feed. Biofloc water and fecal samples were collected from all tanks at time 0 (T0, study day 15) and T7, T70, and T140; prokaryotic and eukaryotic abundance and diversity were assessed using high-throughput amplicon sequencing of the 16S and 18S rRNA genes, respectively. Fecal 16S microbiome in all treatments was dominated by Fusobacteria (namely Cetobacterium) with minority representation by Proteobacteria, Firmicutes, Bacteroidetes, and Planctomycetes. Opisthokonts (namely Capsaspora) were the dominant eukaryote detected overall in all fecal samples. Fecal 16S and 18S relative abundances varied significantly with time. Relative abundance of fecal 16S differed significantly between Control and P-Free+Phytase feed treatments only at T140 (harvest). Fecal 18S relative abundance differences among feed treatments were detected only at T0 and T7 and only at the supergroup taxonomic level. Prokaryotic communities in biofloc water among feed treatments and across times were highly diverse and dominated by Proteobacteria, Bacteroidetes, Fusobacteria, Chloroflexi, Planctomycetes, and Actinobacteria. High relative abundances of Capsaspora across time characterized eukaryotic communities. Relative abundances of 16S and 18S taxa in water varied significantly over time. Control and P-Free feed 16S relative abundances in water differed significantly at T0 and T7. Time was the factor that explained most of the variation observed for 16S and 18S beta diversity. Overall, results of the present experiment suggest minimal influence of phytase-treated or dicalcium phosphate-free feeds on hybrid tilapia 16S and 18S water and fecal microbiomes throughout the experiment, particularly because the base feed formulation was the same for all treatments. During this experiment and at harvest tilapia in all treatments appeared healthy and robust, and no known pathogenic bacteria or eukaryotes were detected in any sample, suggesting the observed microbiomes may represent system-specific “healthy” core microbiomes.

Microbial spatiotemporal succession and metabolic difference in multidimensional pit mud used for the production of Luzhou-flavor baijiu

Pit mud (PM) prokaryotic community is essential for the solid-fermentation of Luzhou-flavor baijiu. In this study, the multidimensional (four vertical positions) microbial communities of different PMs were investigated. Microbial communities were significantly different in multidimensional PMs (p = 0.001). Horizontally speaking, the relative abundance of Longilinea at the position 1 (bottom of the cellar) was highest in 30-year PMs (16.19%) and decreased gradually in 100- (11.95%) and 300-year (0.27%) PMs. Methanobrevibacter had the highest relative abundance at the position 3 (up the huangshui fluid) in 100-year PMs (18.98%), and decreased in 300-year PMs (8.73%), at the position 4 (top site of the cellar), Clostridium had the highest abundance in 100-year PMs (8.24%). Vertically speaking, Petrimonas had the highest abundance (17.4%) at the position 3 in 100-year PMs, while for the 300-year PMs, Lactobacillus and Caproiciproducens had the highest abundance at the position 1. RDA analysis indicated that lactic, caproic, butyric, and acetic acids were the four key physicochemical factors. Amino acids, peptides, fatty acids, and conjugates were the main metabolites of PMs, and S-Acetyldihydrolipoamide-E, succinic acid, aspartic acid, asparagine and valine were key differential metabolites. Based on OPLS-DA analysis, 20 differential flavor compounds were identified, mainly including esters such as hexanoic acid methyl ester, ethyl acetate, hexanoic acid ethyl ester, butanoic acid hexyl ester and acids such as hexanoic acid, butanoic acid and heptanoic acid. Moreover, hexanoic, octanoic acid and their corresponding esters were concentrated on 300-year PMs. This study provides theoretical support for improving the quality of PM.

Application of full-scale aerobic granular sludge technology for removing nitrate from groundwater intended for human consumption

The dependence on groundwater for human consumption has increased worldwide in the last decades. Nitrate (NO3−) often reaches groundwater and causes significant degradation in groundwater quality. In an effort to address this issue, a full-scale water treatment plant using aerobic granular sludge (AGS) technology was built to remove NO3− from nitrate-polluted groundwater intended for human consumption in a rural village. The impact of changes in the operational conditions of hydraulic retention time (HRT) and organic matter loading (OML) rate on NO3− removal, overall system performance, and the granule microbiome were studied. Regardless of the HRT, the AGS technology was successful in removing NO3− with removal rates >50 % with an optimal OML rate of 75 mg L−1. No significant variations in the total abundance of any of the denitrification genes were observed. The composition of prokaryotic and eukaryotic communities was affected by changes in the HRT and OML rate. Specific prokaryotic taxa were identified as responsive to changes in operational parameters and their abundances were linked to the removal of NO3−, confirming that the microbes are critical to the NO3− removal process. This study demonstrates that the AGS technology can be successfully implemented to treat nitrate-polluted groundwater in rural villages to produce water of drinking quality. In addition, the reported hydraulic retention times and organic matter loading rate can be used to further improve the system performance to remove nitrate from groundwater.

Phylogenetic Diversity of Prokaryotic Communities of the Upper Sediment Layers of the Kandalaksha Bay, White Sea

Phylogenetic Diversity of Prokaryotic Communities of the Upper Sediment Layers of the Kandalaksha Bay, White Sea

Profiling Prokaryotic Communities and Aaptamines of Sponge Aaptos suberitoides from Tulamben, Bali.

Sponges (Porifera) harbor a diversity of microorganisms that contribute largely to the production a vast array of bioactive compounds. The microorganisms associated with sponge have an important impact on the chemical diversity of the natural products. Herein, our study focuses on an Aaptos suberitoides commonly found in Indonesia. The objective of this study was to investigate the profile of prokaryotic community and the presence of aaptamine metabolites in sponge Aaptos suberitoides. Sponges were collected from two site locations (Liberty Wreck and Drop Off) in Tulamben, Bali. The sponges were identified by barcoding DNA cytochrome oxidase subunit I (COI) gene. The profile of prokaryotic composition was investigated by amplifying the 16S rRNA gene using primers 515f and 806r to target the V4 region. The metabolites were analyzed using LC-MS, and dereplication was done to identify the aaptamines and its derivates. The barcoding DNA of the sponges confirmed the identity of samples as Aaptos suberitoides. The prokaryotic communities of samples A. suberitoides were enriched and dominated by taxa Proteobacteria, Chloroflexi, Actinobacteria, and Acidobacteria. The chemical analysis showed that all sponges produce aaptamine and isoaaptamine except A. suberitoides S2421 produce analog of aaptamines. This is the first report on the profile of prokaryotic community and the aaptamine of tropical marine sponges, A. suberitoides, from Tulamben, Bali.

Soil prokaryotic characterization in response to natural moisture gradient in the temperate grassland ecosystems

Abstract Soil moisture, which is an important factor affecting ecosystem function, can maintain microbial activity and ultimately change the microbial community by altering vegetation diversity and controlling the diffusion and transport of soil nutrients. To explore the effects of soil water content (SWC) on soil prokaryotic community, we established a study area covering a natural soil moisture gradient and subdivided it into high (HW, 4.80 ± 1.18%), medium (MW, 2.17 ± 0.09%) and low water contents (LW, 1.85 ± 0.14%) in the grassland ecosystem along the south shore of Hulun Lake in Inner Mongolia, China. Environmental factors were determined by field surveys and laboratory analyses. Soil prokaryotes were determined by high-throughput sequencing techniques. Vegetation characteristics and soil physicochemical properties had a significant effect on prokaryotic richness diversity, and SWC was the most important factor influencing prokaryotic richness diversity. In the MW, the number of differential prokaryotes was lowest, and prokaryotic microorganisms had the highest diversity and relative abundance at the phylum level, which may reflect less intrinsic variation and higher overall activity of the prokaryotic community in the MW. In addition, HW and LW had lower prokaryotic diversity and relative abundance at the phylum level, and phenotypic predictions for both groups indicated a more tolerant prokaryotic community. In summary, the prokaryotic community responded significantly to the natural moisture gradients in grassland ecosystems along the south shore of Hulun Lake, and both too high and too low soil moisture increased prokaryotic stress resistance.

Metagenome-assembled genomes reveal greatly expanded taxonomic and functional diversification of the abundant marine Roseobacter RCA cluster

BackgroundThe RCA (Roseobacter clade affiliated) cluster belongs to the family Roseobacteracea and represents a major Roseobacter lineage in temperate to polar oceans. Despite its prevalence and abundance, only a few genomes and one described species, Planktomarina temperata, exist. To gain more insights into our limited understanding of this cluster and its taxonomic and functional diversity and biogeography, we screened metagenomic datasets from the global oceans and reconstructed metagenome-assembled genomes (MAG) affiliated to this cluster.ResultsThe total of 82 MAGs, plus five genomes of isolates, reveal an unexpected diversity and novel insights into the genomic features, the functional diversity, and greatly refined biogeographic patterns of the RCA cluster. This cluster is subdivided into three genera: Planktomarina, Pseudoplanktomarina, and the most deeply branching Candidatus Paraplanktomarina. Six of the eight Planktomarina species have larger genome sizes (2.44–3.12 Mbp) and higher G + C contents (46.36–53.70%) than the four Pseudoplanktomarina species (2.26–2.72 Mbp, 42.22–43.72 G + C%). Cand. Paraplanktomarina is represented only by one species with a genome size of 2.40 Mbp and a G + C content of 45.85%. Three novel species of the genera Planktomarina and Pseudoplanktomarina are validly described according to the SeqCode nomenclature for prokaryotic genomes. Aerobic anoxygenic photosynthesis (AAP) is encoded in three Planktomarina species. Unexpectedly, proteorhodopsin (PR) is encoded in the other Planktomarina and all Pseudoplanktomarina species, suggesting that this light-driven proton pump is the most important mode of acquiring complementary energy of the RCA cluster. The Pseudoplanktomarina species exhibit differences in functional traits compared to Planktomarina species and adaptations to more resource-limited conditions. An assessment of the global biogeography of the different species greatly expands the range of occurrence and shows that the different species exhibit distinct biogeographic patterns. They partially reflect the genomic features of the species.ConclusionsOur detailed MAG-based analyses shed new light on the diversification, environmental adaptation, and global biogeography of a major lineage of pelagic bacteria. The taxonomic delineation and validation by the SeqCode nomenclature of prominent genera and species of the RCA cluster may be a promising way for a refined taxonomic identification of major prokaryotic lineages and sublineages in marine and other prokaryotic communities assessed by metagenomics approaches.4nWA41D1uUohyPVze8XWvDVideo