Total 16S rRNA Gene Research Articles

Ecological processes shaping highly connected bacterial communities along strong environmental gradients.

Along the river-sea continuum, microorganisms are directionally dispersed by water flow while being exposed to strong environmental gradients. To compare the two assembly mechanisms that may strongly and differently influence metacommunity dynamics, namely homogenizing dispersal and heterogeneous selection, we characterized the total (16S rRNA gene) and putatively active (16S rRNA transcript) bacterial communities in the Pearl River-South China Sea Continuum, during the wet (summer) and dry (winter) seasons using high-throughput sequencing. Moreover, well-defined sampling was conducted by including freshwater, oligohaline, mesohaline, polyhaline, and marine habitats. We found that heterogeneous selection exceeded homogenizing dispersal in both the total and active fractions of bacterial communities in two seasons. However, homogeneous selection was prevalent (the dominant except in active bacterial communities during summer), which was primarily due to the bacterial communities' tremendous diversity (associated with high rarity) and our specific sampling design. In either summer or winter seasons, homogeneous and heterogeneous selection showed higher relative importance in total and active communities, respectively, implying that the active bacteria were more responsive to environmental gradients than were the total bacteria. In summary, our findings provide insight into the assembly of bacterial communities in natural ecosystems with high spatial connectivity and environmental heterogeneity.

Real-time PCR-based quantitative microbiome profiling elucidates the microbial dynamic succession in backslopping fermentation of Taiwanese pickled cabbage.

Microbiota succession determines the flavor and quality of fermented foods. Quantitative PCR-based quantitative microbiome profiling (QMP) has been applied broadly for microbial analysis from absolute abundance perspectives, transforming microbiota ratios into counts by normalizing 16S ribosomal RNA (16S rRNA) gene sequencing data with gene copies quantified by quantitative PCR. However, the application of QMP in fermented foods is still limited. QMP elucidated microbial succession of Taiwanese pickled cabbage. In the spontaneous first-round fermentation (FR), the 16S rRNA gene copies of total bacteria increased from 6.1 to 10 log copies mL-1. The dominant lactic acid bacteria genera were successively Lactococcus, Leuconostoc and Lactiplantibacillus. Despite the decrease in the proportion of Lactococcus during the succession, the absolute abundance of Lactococcus still increased. In the backslopping second-round fermentation (SR), the total bacteria 16S rRNA gene copies increased from 7.6 to 9.9 log copies mL-1. The addition of backslopping starter and vinegar rapidly led to a homogenous microbial community dominated by Lactiplantibacillus. The proportion of Lactiplantibacillus remained consistently around 90% during SR, whereas its absolute abundance exhibited a continuous increase. In SR without vinegar, Leuconostoc consistently dominated the fermentation. The present study highlights that compositional analysis would misinterpret microbial dynamics, whereas QMP reflected the real succession profiles and unveiled the essential role of vinegar in promoting Lactiplantibacillus dominance in backslopping fermentation of Taiwanese pickled cabbage. Quantitative microbiome profiling (QMP) was found to be a more promising approach for the detailed observation of microbiome succession in food fermentation compared to compositional analysis. © 2024 Society of Chemical Industry.

Increased prokaryotic diversity in the Red Sea deep scattering layer

BackgroundThe diel vertical migration (DVM) of fish provides an active transport of labile dissolved organic matter (DOM) to the deep ocean, fueling the metabolism of heterotrophic bacteria and archaea. We studied the impact of DVM on the mesopelagic prokaryotic diversity of the Red Sea focusing on the mesopelagic deep scattering layer (DSL) between 450–600 m.ResultsDespite the general consensus of homogeneous conditions in the mesopelagic layer, we observed variability in physico-chemical variables (oxygen, inorganic nutrients, DOC) in the depth profiles. We also identified distinct seasonal indicator prokaryotes inhabiting the DSL, representing between 2% (in spring) to over 10% (in winter) of total 16S rRNA gene sequences. The dominant indicator groups were Alteromonadales in winter, Vibrionales in spring and Microtrichales in summer. Using multidimensional scaling analysis, the DSL samples showed divergence from the surrounding mesopelagic layers and were distributed according to depth (47% of variance explained). We identified the sources of diversity that contribute to the DSL by analyzing the detailed profiles of spring, where 3 depths were sampled in the mesopelagic. On average, 7% was related to the epipelagic, 34% was common among the other mesopelagic waters and 38% was attributable to the DSL, with 21% of species being unique to this layer.ConclusionsWe conclude that the mesopelagic physico-chemical properties shape a rather uniform prokaryotic community, but that the 200 m deep DSL contributes uniquely and in a high proportion to the diversity of the Red Sea mesopelagic.

Inhibitory Effects of Ammonia on Archaeal 16S rRNA Transcripts in Thermophilic Anaerobic Digester Sludge

High temperatures exacerbate the ammonia inhibition of anaerobic digestion coupled with methanogenesis. The inhibition of methane production by ammonia has been observed in other studies. However, the underlying mechanism is not well understood and requires further investigation. This study explored the effect of ammonia stress on archaeal 16S rRNA transcripts in thermophilic anaerobic digester sludge. Different ammonium concentrations were checked for their influence on the methanogenic rate and hydrogen accumulation. Quantitative PCR was used to compare the changes in total archaeal 16S rRNA expression. A Monte Carlo permutation test within redundancy analysis (RDA) was adopted for exploring the relationship between environmental variables and archaeal 16S rRNA and their transcripts. The results showed that with the increase in ammonium concentration, the methanogenic rate decreased and hydrogen accumulation occurred. The total archaeal 16S rRNA genes and transcripts copy numbers decreased significantly in treatments with higher ammonium concentrations (7 and 10 g NH4+-N/L), but did not change much at lower ammonia concentrations (3 g NH4+-N/L) compared with the 0 g NH4+-N/L treatment. The RDA analysis further revealed that most environmental variables, including ammonia and methane, except for formate, were significantly correlated with the community structure activity of archaeal 16S rRNA transcripts rather than the community structure of their genes. The composition of archaeal 16S rRNA transcripts showed that the hydrogenotrophic methanogen Methanothermobacter dominated the methanogenic community activity in all incubations. It exhibited sensitivity to ammonia stress and should be responsible for the methanogenic inhibition under thermophilic conditions. Our findings suggested that archaeal 16S rRNA transcripts, rather than 16S rRNA genes, are key indicators of ammonia stress and methanogenic activity.

The microbial removal of bisphenols in aquatic microcosms and associated alteration in bacterial community.

The concept of the study resulted from numerous concerns around bisphenol A (BPA) and bisphenol S (BPS) in aquatic environments. In this study, river water and sediment microcosms highly polluted with bisphenols and bioaugmented with two BPs-removing bacterial strains were constructed. The study aimed to determine the rate of high-concentrated BPA and BPS (BPs) removal from river water and sediment microniches, and the effect of water bioaugmentation with bacterial consortium on the removal rates of these pollutants. Moreover, the impact of introduced strains and exposure to BPs on the structural and functional composition of the autochthonous bacterial communities was elucidated. Our findings indicate that the removal activity of autochthonous bacteria was sufficient for effectively BPA elimination and reducing BPS content in the microcosms. The number of introduced bacterial cells decreased continuously until day 40, and on consecutive sampling days, no bioaugmented cells were detected. Sequencing analysis of the total 16S rRNA genes revealed that the community composition in bioaugmented microcosms amended with BPs differed significantly from those treated either with bacteria or BPs. A metagenomic analysis found an increase in the abundance of proteins responsible for xenobiotics removal in BPs-amended microcosms. This study provides new insights into the effects of bioaugmentation with a bacterial consortium on bacterial diversity and BPs removal in aquatic environments.

Low nitrogen fertilization enriches nitrogen‐fixing bacteria in the Brassica seed microbiome of subsequent generations

AbstractIntroductionThe consequences of overfertilization on agricultural and native ecosystems are well‐documented, but the impact of reduced fertilization on plant–microbe interactions is less understood. Here, we analysed the impact of different nitrogen (N) fertilization regimes over two subsequent growing seasons on the seed microbiome of winter oilseed rape (Brassica napus L.).Materials and MethodsSeed microbial diversity, composition, and abundance were analysed by a combined approach of amplicon sequencing, quantitative real‐time PCR, and microscopy. A germination assay was conducted to quantify bacteria and nifH genes in roots.ResultsTwo consecutive years of either low or high N fertilization resulted in a significant shift in seed microbiota; nine discriminating bacterial orders and 32 bacterial features were identified. Among them, potentially N‐fixing bacteria (Rhizobiales and Rhizobium) were identified as biomarkers for low N fertilization. Moreover, quantitative measurements revealed that 16S ribosomal RNA (rRNA) and bacterial nifH gene counts were significantly higher under lower N availability. Relative to total 16S rRNA genes, seeds and roots contained 0.002% and 0.3% nifH genes on average, respectively. The alternation of N levels between the first and the second growing season (high to low, or low to high) had, however, no impact on seed microbiota, suggesting that a low N availability for at least two generations is required to enrich N‐fixing taxa in seeds.ConclusionOur study revealed a flexible, environmentally influenced seed microbiome assembly and suggests innovative microbiome management via biological nitrogen fixation to optimize fertilization regimes in future agriculture.

Soil oxytetracycline alters the effects of phosphate fertilisation and Bacillus amyloliquefaciens on the bacterial community of Medicago sativa rhizosphere

Introducing specific plant growth-promoting bacteria (PGPB) into the soil ecological system is vital to improve nutrient utilization efficiency. Suitable combinations of inoculant and fertilisation particularly phosphorus (P) play important roles in enhancing the effects of PGPB. The ecotoxic risks of antibiotics in agro-ecosystems are of great concern. A pot experiment was conducted to explore the effects of P fertilisation, Bacillus amyloliquefaciens inoculation, and oxytetracycline (OTC) on the bacterial community and the genes related to soil nitrogen (N) and phosphorus (P) conversion in the rhizosphere of alfalfa. Soil bacterial biodiversity including the number of species and richness was reduced by P fertilisation and OTC addition, enhanced by the inoculation of B. amyloliquefaciens without OTC addition. OTC increased the correlations among bacterial genera. The abundance of total 16S rRNA genes, N- and P-cycling functional genes was decreased by OTC in most cases, but increased at 0 mg P kg−1 and 160 mg OTC kg−1 (P–OTC+) when the soil was inoculated with B. amyloliquefaciens. The relative abundance of five bacterial genera, including Mesorhizobium and some unitalicise uncultured genera, increased at P–OTC+ when inoculated with B. amyloliquefaciens. These genera might use the necromass of some microbes killed by OTC as a nutrient substrate for enhanced growth, thus enhancing the expression of N- and P-cycling functional genes. Overall, OTC altered the effects of P fertilisation and B. amyloliquefaciens inoculation on the bacterial community, N- and P-cycling functional genes in the rhizosphere of alfalfa.

Bacterial diversity of an acid mine drainage beside the Xichú River (Mexico) accessed by culture-dependent and culture-independent approaches.

Xichú River is a Mexican river located in an environmental preservation area called Sierra Gorda Biosphere Reserve. Around it, there are tons of abandoned mine residues that represent a serious environmental issue. Sediment samples of Xichú River, visibly contaminated by flows of an acid mine drainage, were collected to study their prokaryotic diversity. The study was based on both cultural and non-cultural approaches. The analysis of total 16S rRNA gene by MiSEQ sequencing allowed to identify 182 Operational Taxonomic Units. The community was dominated by Pseudomonadota, Bacteroidota, "Desulfobacterota" and Acidobacteriota (27, 21, 19 and 16%, respectively). Different culture conditions were used focusing on the isolation of anaerobic bacteria, including sulfate-reducing bacteria (SRB) and arsenate-reducing bacteria (ARB). Finally, 16 strains were isolated. Among them, 12 were phylogenetically identified, with two strains being SRB, belonging to the genus Solidesulfovibrio ("Desulfobacterota"), while ten are ARB belonging to the genera Azospira (Pseudomonadota), Peribacillus (Bacillota), Raineyella and Propionicimonas (Actinomycetota). The isolate representative of Raineyella genus probably corresponds to a new species, which, besides arsenate, also reduces nitrate, nitrite, and fumarate.

P380 Changes in faecal microbiome and metabolome are more pronounced in Crohn’s disease patients who adhered to the CD-TREAT diet and responded by calprotectin.

Abstract Background Treatment with the CD-TREAT solid food diet improves disease activity indices, faecal calprotectin (FCAL) levels and quality of life in adults and children with active Crohn’s disease (CD); particularly in patients who adhere to the diet. Here we describe changes in faecal microbiome parameters during therapy with CD-TREAT and explore these changes against adherence. Methods Children and adult patients with active CD completed an 8-week treatment with CD-TREAT. The levels of FCAL, pH, total sulphide (colorimetry), short chain fatty acids (SCFA), branched chain fatty acids (BCFA) (gas chromatography), total bacterial load (qPCR for total 16S rRNA gene copy number/g) were measured in baseline faecal samples and at four and eight weeks of CD-TREAT. Liquid chromatography mass spectrometry (LC-MS) faecal metabolomics and 16s rRNA sequencing of the faecal microbiome were performed at the same timepoints. Since CD-TREAT is gluten-free, detection of the gluten immunogenic peptide (GIP) in faeces was used as an objective biomarker of treatment adherence. Data are presented as median (IQR). Results Forty patients [17 children, age: 14.0 (11.3-15.1) years; 23 adults, age: 33.9 (27.8-45.9) years] participated. Eighteen (45%) patients had detectable GIP in at least one of the two follow-up timepoints, suggesting incomplete adherence; the remaining 22 (55%) patients had undetectable GIP throughout the treatment course. Baseline FCAL levels decreased significantly in the group of patients with undetectable GIP [mg/kg, baseline: 1,190 (3,611-129); 8 weeks: 534 (92-1,230), p<0.05] but not in patients with detectable GIP [mg/kg, baseline: 599 (328-1,857); 8 weeks: 702 (278-1,496)]. During CD-TREAT, the concentration of faecal acetate, propionate, butyrate, total sulphide, total microbial load and faecal pH significantly changed in those with undetectable GIP but were less pronounced where GIP was detectable (Figure 1). Shannon diversity and richness significantly increased at both genus and OTU level, the abundance of several taxa changed, and LC-MS faecal metabolome shifted during CD-TREAT, but only in those with undetectable GIP (Figures 2 & 3). Conclusion We have identified that full adherence with CD-TREAT only occurs in ~55% of recipients, however a significant reduction in calprotectin is seen in those who adhere, and this is associated with microbial and metabolic changes which parallel those seen in successful exclusive enteral nutrition.

Influence of DNA from non-viable sources on the riverine water and biofilm microbiome, resistome, mobilome, and resistance gene host assignments

Shotgun metagenomic studies have revealed the diversity, relative abundance, and hosts of antibiotic resistance genes (ARGs) across environmental matrices. There is motivation to combine this method with viability-based techniques to better define ARG hazard. The objectives of this study were to evaluate the performance of different methods for extracellular DNA (eDNA) and putative “non-viable” cell DNA separation to understand the influence on ARG-host assignments. Paired water and biofilm samples were collected along a land use gradient. To study putative “viable-cell” DNA, samples were treated with propidium monoazide (i.e., PMA-DNA). To study eDNA, intracellular and extracellular DNA were separated. qPCR revealed differences in total 16S rRNA gene copies in water for filter vs. centrifuge-concentrated samples, but otherwise there were no differences in gene copy concentrations between DNA fractions. Next, metagenomic sequencing was performed on PMA-DNA and total DNA extracts revealing significant differences between the two for bacterial community structure and ARG profiles. Putative viable taxa containing pathogenic ARG hosts were identified in biofilm and water. Removing PMA-bound DNA improved N50 and assembly mapping compared to total DNA extracts. This study demonstrates the impact of different sample preparation methods on informing the hazard potential associated with riverine ARGs in water and biofilm.

Composition of Prokaryotic Communities in Anaerobic Enrichment Cultures of Crude Oil from Romashkino Oilfield (Russia)

Despite the many papers published on oilfield ecosystems, there is a lack of data about microbial community structure and functioning in many crude oils or oilfields and wells. One of such poorly studied oilfields is supergiant Romashkino situated in Tatarstan (Russia). In the present study, prokaryotic community composition and abundance of functional genes encoding sulfate reduction and rhamnolipid production, was investigated in enrichment cultures of four samples from Romashkino oilfield production wells with different oil/water ratios. The enrichment was conducted under anaerobic conditions, sulfate and nitrate were used as electron acceptors, and acetate – as an electron donor. In enrichment culture A and enrichment culture B, bacteria of the Pseudomonadaceae family predominated with 99% and 93% relative abundance, respectively. In enrichment culture C (obtained on the basis of initial sample contained oil with medium water content) and D (obtained on the basis of initial sample contained oil with very high water content), Pseudomonadaceae were one of the two predominating families, along with Micrococcaceae (enrichment culture C) and Dietziaceae (enrichment culture D). The proportion of dsrA and apsA genes encoding sulfate reduction to 16S rRNA gene copy numbers was quite low and ranged between 0.003% (enrichment cultures A, B) and 0.027% (enrichment culture D). The proportion of rhlB gene encoding rhamnolipid production from the total 16S rRNA gene copy number was 1.10% in sample A and 0.06% in sample B. In enrichment cultures C and D the rhlB gene was not found.

Exploring the effect of a microencapsulated citrus essential oil on in vitro fermentation kinetics of pig gut microbiota.

Essential oils (EOs) have emerged as a potential alternative to antibiotics in pig breeding due to their antimicrobial properties. Citrus EOs, a common by-product of the orange juice industry, can be an interesting alternative from a financial perspective due to their huge offer in the global market. Thus, the effect of a citrus EO, and specifically different formulations of Brazilian Orange Terpenes (BOT), on pig gut microbiota was evaluated by means of an in vitro fermentation model simulating different sections of the pig gut (stomach, ileum, and colon). Treatments consisted in: BOT in its unprotected form (BOT, 1.85 and 3.70 mg/mL), microencapsulated BOT (MBOT, 3.50 and 7.00 mg/mL), colistin (2 μg/mL), and a control. BOT and MBOT altered in a similar way the total bacterial 16S rRNA gene copies in the stomach only from 18 h of incubation onwards, and no metabolite production in terms of short-chain fatty acids (SCFAs) was detected. In ileal and colonic fermentations, BOT and MBOT affected ileal and colonic microbiota in terms of total bacterial 16S rRNA gene copies, reduced phylogenetic diversity, and altered composition (p < 0.05) as evidenced by the significant reduction of certain bacterial taxa. However, more pronounced effects were found for MBOT, indicating its higher antimicrobial effects compared to the unprotected BOT, and suggesting that the antibacterial efficiency of the unprotected BOT was probably enhanced by microencapsulation. Furthermore, MBOT stimulated lactate production in ileal fermentations and greatly stimulated overall SCFA production in colonic fermentations. This indicates that besides the shifts in ileal and colonic microbiota by the delivered EO (BOT), the wall material of microcapsules (chitosan/modified starch) might have worked as an additional carbon source with prebiotic functioning, stimulating growth and metabolic activity (SCFAs) of colonic bacteria.

Bioaugmentation with methanogens cultured in a micro-aerobic microbial community for overloaded anaerobic digestion recovery

Anaerobic digestion (AD) is widely used for conversion of waste materials into biogas, but inhibition of methane production caused by overloading can be a major problem. The micro-aerobic microbial community MC1 was used to successfully culture methanogens, Methanosarcina acetivorans C2A and Methanosaeta thermophila NBRC 101360. The maximum 16S rRNA gene concentrations of Methanosarcina acetivorans C2A and Methanosaeta thermophila NBRC101360 were 1.06 × 106 and 1.35 × 103 copies/mL, respectively. The five key bacteria in MC1 were quantified to assess the effect of inoculation on the abundances of the bacteria in the mixed culture. The original MC1 total 16S rRNA gene concentration was 1.93 × 108 copies/mL, and the total 16S rRNA gene concentration had increased to 4.79 × 109 copies/mL on day 9 (p < 0.05). The proportions of the key strains in MC1+MST had changed by day 9. Cells were harvested and used to bioaugment and increase the pH values of the high- and medium-temperature anaerobic systems. After bioaugmentation, thermophilic AD recovered well. The cumulative amounts of gas produced were 44.78% and 28.28% higher in the MC1+MST and MC1 groups, respectively, than the sterilized control. The MC1+MST group gave better results than the chemical addition control group (CaCO3). There was no clear effect of bioaugmentation in mesophilic AD. When compared with traditional pure culture of methanogens as inoculants, methanogen cultivation in MC1 was simple and there was no need to separate and purify the target strains. This simplified methanogenic bioaugmentation agent was useful to study the mechanism of bioaugmentation for the recovery from low pH inhibition, showing the potential for practical application.

Biogeography of Southern Ocean Active Prokaryotic Communities Over a Large Spatial Scale.

The activity of marine microorganisms depends on community composition, yet, in some oceans, less is known about the environmental and ecological processes that structure their distribution. The objective of this study was to test the effect of geographical distance and environmental parameters on prokaryotic community structure in the Southern Ocean (SO). We described the total (16S rRNA gene) and the active fraction (16S rRNA-based) of surface microbial communities over a ~6,500 km longitudinal transect in the SO. We found that the community composition of the total fraction was different from the active fraction across the zones investigated. In addition, higher α-diversity and stronger species turnover were displayed in the active community compared to the total community. Oceanospirillales, Alteromonadales, Rhodobacterales, and Flavobacteriales dominated the composition of the bacterioplankton communities; however, there were marked differences at the order level. Temperature, salinity, silicic acid, particulate organic nitrogen, and particulate organic carbon correlated with the composition of bacterioplankton communities. A strong distance–decay pattern between closer and distant communities was observed. We hypothesize that it was related to the different oceanic fronts present in the Antarctic Circumpolar Current. Our findings contribute to a better understanding of the complex arrangement that shapes the structure of bacterioplankton communities in the SO.

Multidrug-resistant epi-endophytic bacterial community in Posidonia oceanica of Mahdia coast as biomonitoring factor for antibiotic contamination.

Faced with the significant disturbances, mainly of anthropogenic origin, which affect the Mediterranean coastal ecosystem, Posidonia oceanica (L.) Delile has often been used to assess the state of health of this environment. The present study aims to determine the multidrug resistance patterns among isolated and identified epi-endophytic bacterial strains in P. oceanica seagrass collected from Mahdia coastal seawater (Tunisia). To investigate the bacterial community structure and diversity from coastal seawater samples from Mahdia, total DNA extraction and 16S rRNA gene amplification were performed and analyzed by denaturing gradient gel electrophoresis (DGGE). The DGGE profiles showed that some bands were specific to a given site, while other bands were found to be common to more than one sample. In the other hand, bacterial strains were isolated from 1mL of leaves and epiphytes suspension of P. oceanica seagrass in marine agar. Forty-three isolates were obtained, seven of them were selected and identified on the basis of 16S rRNA gene sequence analysis. These isolates belonged to the genus Bacillus, exhibiting 98-100% of identity with known sequences. Susceptibility patterns of these strains were studied toward commonly used antibiotics in Tunisia. All identified isolates were resistant to Aztreonam (72.1%), Ceftazidime (60.5%), Amoxicillin (56%) and Rifampicin (51.2%). S5-L13 strain had presented the highest multidrug resistance with a MAR index of 0.67.

Occurrence of opportunistic pathogens in private wells after major flooding events: A four state molecular survey

Private wells can become contaminated with waterborne pathogens during flooding events; however, testing efforts focus almost exclusively on fecal indicator bacteria. Opportunistic pathogens (OPs), which are the leading cause of identified waterborne disease in the United States, are understudied in private wells. We conducted a quantitative polymerase chain reaction survey of Legionella spp., L. pneumophila, Mycobacterium spp., M. avium, Naegleria fowleri, and shiga toxin-producing Escherichia coli gene markers and total coliform and E. coli in drinking water supplied by private wells following the Louisiana Floods (2016), Hurricane Harvey (2017), Hurricane Irma (2017), and Hurricane Florence (2018). Self-reported well characteristics and recovery status were collected via questionnaires. Of the 211 water samples collected, 40.3% and 5.2% were positive for total coliform and E. coli, which were slightly elevated positivity rates compared to prior work in coastal aquifers. DNA markers for Legionella and Mycobacterium were detected in 54.5% and 36.5% of samples, with L. pneumophila and M. avium detected in 15.6% and 17.1%, which was a similar positivity rate relative to municipal system surveys. Total bacterial 16S rRNA gene copies were positively associated with Legionella and Mycobacterium, indicating that conditions that favor occurrence of general bacteria can also favor OPs. N. fowleri DNA was detected in 6.6% of samples and was the only OP that was more prevalent in submerged wells compared to non-submerged wells. Self-reported well characteristics were not associated with OP occurrence. This study exposes the value of routine baseline monitoring and timely sampling after flooding events in order to effectively assess well water contamination risks.

T4-like Phages Reveal the Potential Role of Viruses in Soil Organic Matter Mineralization.

Viruses are the most abundant biological entities in the world, but their ecological functions in soil are virtually unknown. We hypothesized that greater abundance of T4-like phages will increase bacterial death and thereby suppress soil organic carbon (SOC) mineralization. A range of phage and bacterial abundances were established in sterilized soil by reinoculation with 10-3 and 10-6 dilutions of suspensions of unsterilized soil. The total and viable 16S rRNA gene abundance (a universal marker for bacteria) was measured by qPCR to determine bacterial abundance, with propidium monoazide (PMA) preapplication to eliminate DNA from non-viable cells. Abundance of the g23 marker gene was used to quantify T4-like phages. A close negative correlation between g23 abundance and viable 16S rRNA gene abundance was observed. High abundance of g23 led to lower viable ratios for bacteria, which suggested that phages drove microbial necromass production. The CO2 efflux from soil increased with bacterial abundance but decreased with higher abundance of T4-like phages. Elimination of extracellular DNA by PMA strengthened the relationship between CO2 efflux and bacterial abundance, suggesting that SOC mineralization by bacteria is strongly reduced by the T4-like phages. A random forest model revealed that abundance of T4-like phages and the abundance ratio of T4-like phages to bacteria are better predictors of SOC mineralization (measured as CO2 efflux) than bacterial abundance. Our study provides experimental evidence of phages' role in organic matter turnover in soil: they can retard SOC decomposition but accelerate bacterial turnover.

Biogeography of ammonia oxidizers in New England and Gulf of Mexico salt marshes and the potential importance of comammox

Few studies have focused on broad scale biogeographic patterns of ammonia oxidizers in coastal systems, yet understanding the processes that govern them is paramount to understanding the mechanisms that drive biodiversity, and ultimately impact ecosystem processes. Here we present a meta-analysis of 16 years of data of ammonia oxidizer abundance, diversity, and activity in New England (NE) salt marshes and 5 years of data from marshes in the Gulf of Mexico (GoM). Potential nitrification rates were more than 80x higher in GoM compared to NE marshes. However, nitrifier abundances varied between regions, with ammonia-oxidizing archaea (AOA) and comammox bacteria significantly greater in GoM, while ammonia-oxidizing bacteria (AOB) were more than 20x higher in NE than GoM. Total bacterial 16S rRNA genes were also significantly greater in GoM marshes. Correlation analyses of rates and abundance suggest that AOA and comammox are more important in GoM marshes, whereas AOB are more important in NE marshes. Furthermore, ratios of nitrifiers to total bacteria in NE were as much as 80x higher than in the GoM, suggesting differences in the relative importance of nitrifiers between these systems. Communities of AOA and AOB were also significantly different between the two regions, based on amoA sequences and DNA fingerprints (terminal restriction fragment length polymorphism). Differences in rates and abundances may be due to differences in salinity, temperature, and N loading between the regions, and suggest significantly different N cycling dynamics in GoM and NE marshes that are likely driven by strong environmental differences between the regions.

Hydrostatic pressure influence activity and assembly of bacterial communities in reservoir sediments

Abstract Reservoir sediments are subjected to highly variable hydrostatic pressures, but little is known about the direct impacts of this environmental variable on microbial communities and biogeochemical processes mediated by microbes in the numerous deep reservoirs (&gt;100 m) scattered across our planet. To address this gap, the organic matter degradation and community assembly of sediment bacteria were studied in bioreactors maintained under different hydrostatic pressures (0.5–3.0 MPa) and explored using 16S rRNA amplicon sequencing analysis. Our results showed that rates of CO2 and CH4 production and microbial activity decreased significantly with increasing pressure, at least when exceeding 1.0 MPa. In contrast, α‐diversity and community structure of the active (16S rRNA) and total (16S rRNA gene) bacterial communities did not show any significant response to the different hydrostatic pressures, but a co‐occurrence network demonstrated that interactions between bacterial populations were stronger at higher pressures (≥1.5 MPa). Moreover, ecological null model analyses revealed that when the pressure exceeded 1.5 MPa, the main assembly processes of bacterial communities changed from stochastic to deterministic. These findings corroborate an important role of pressure in the assembly and emerging interactions within sediment bacterial communities. Our results imply that increased hydrostatic pressure caused by dam constructions may hamper the metabolism of the sediment microbiota, and that this may result in enhanced sediment burial of nutrients and organic matter, at least when pressures exceed 1.0 MPa.

Patterns of Relative and Quantitative Abundances of Marine Bacteria in Surface Waters of the Subtropical Northwest Pacific Ocean Estimated With High-Throughput Quantification Sequencing.

Bacteria play a pivotal role in shaping ecosystems and contributing to elemental cycling and energy flow in the oceans. However, few studies have focused on bacteria at a trans-basin scale, and studies across the subtropical Northwest Pacific Ocean (NWPO), one of the largest biomes on Earth, have been especially lacking. Although the recently developed high-throughput quantitative sequencing methodology can simultaneously provide information on relative abundance, quantitative abundance, and taxonomic affiliations, it has not been thoroughly evaluated. We collected surface seawater samples for high-throughput, quantitative sequencing of 16S rRNA genes on a transect across the subtropical NWPO to elucidate the distribution of bacterial taxa, patterns of their community structure, and the factors that are potentially important regulators of that structure. We used the quantitative and relative abundances of bacterial taxa to test hypotheses related to their ecology. Total 16S rRNA gene copies ranged from 1.86 × 108 to 1.14 × 109 copies L−1. Bacterial communities were distributed in distinct geographical patterns with spatially adjacent stations clustered together. Spatial considerations may be more important determinants of bacterial community structures than measured environmental variables. The quantitative and relative abundances of bacterial communities exhibited similar distribution patterns and potentially important determinants at the whole-community level, but inner-community connections and correlations with variables differed at subgroup levels. This study advanced understanding of the community structure and distribution patterns of marine bacteria as well as some potentially important determinants thereof in a subtropical oligotrophic ocean system. Results highlighted the importance of considering both the quantitative and relative abundances of members of marine bacterial communities.