Dominant Phylotypes Research Articles

Plant species and associated root nutritional traits influence soil dominant bacteria in coastal wetlands across China.

Climate and edaphic properties drive the biogeographic distribution of dominant soil microbial phylotypes in terrestrial ecosystems. However, the impact of plant species and their root nutritional traits on microbial distribution in coastal wetlands remains unclear. Here, we investigated the nutritional traits of 100 halophyte root samples and the bacterial communities in the corresponding soil samples from coastal wetlands across eastern China. This study spans 22° of latitude, covering over 2500 km from north to south. We found that 1% of soil bacterial phylotypes accounted for nearly 30% of the soil bacterial community abundance, suggesting that a few bacterial phylotypes dominated the coastal wetlands. These dominated phylotypes could be grouped into three ecological clusters as per their preference over climatic (temperature and precipitation), edaphic (soil carbon and nitrogen), and plant factors (halophyte vegetation, root carbon, and nitrogen). We further provide novel evidence that plant root nutritional traits, especially root C and N, can strongly influence the distribution of these ecological clusters. Taken together, our study provides solid evidence of revealing the dominance of specific bacterial phylotypes and the complex interactions with their environment, highlighting the importance of plant root nutritional traits on biogeographic distribution of soil microbiome in coastal wetland ecosystems.

Environmental preferences of soil microbial attributes for long-term nitrogen and acid addition: From phylotype to community

The impact of human-induced nitrogen (N) enrichment on microbial diversity has been extensively studied, with two main hypotheses proposed: soil N availability and soil acidification. However, the specific roles of these two hypotheses and their environmental preferences on soil bacterial and fungal communities are not fully understood. By conducting two independent experiments (a 16-year N and a 6-year acid addition) in a temperate semi-arid grassland, we tested the responses of soil microbial attributes (e.g., richness and relative abundance) at various levels (community, phylum/class, and phylotype) to N and acid addition. At the community level, our results showed that both N and acid addition had a negative effect on the richness of the whole, dominant, and rare bacterial communities; N enrichment only decreased the richness of the dominant fungal community, while acid addition decreased the richness of the whole, dominant, and rare fungal communities. By categorizing the microbial attributes into nine environmental preferences based on their responses to N and acid addition, we found that most bacterial phyla were associated with low N availability and high pH preferences, while most fungal classes had other environmental preferences. Most dominant bacterial phylotypes were linked to low N availability and high pH preferences, while most dominant fungal phylotypes were associated with other environmental preferences and high pH preferences. Conversely, most rare bacterial and fungal phylotypes were linked to other environmental preferences. Our experiments revealed that the decline in bacterial richness caused by N enrichment was predominantly due to their sensitivity to soil acidification, while fungal richness remained largely unaltered. By pinpointing distinct microbial attributes at different levels in response to N and acid addition, our findings could potentially forecast how soil microorganisms will react to future global N deposition.

Comparative evaluation of 16S rRNA primer pairs in identifying nitrifying guilds in soils under long-term organic fertilization and water management.

Compared with 454 sequencing technology, short-read sequencing (e.g., Illumina) technology generates sequences of high accuracy, but limited length (<500 bp). Such a limitation can prove that studying a target gene using a large amplicon (>500 bp) is challenging. The ammonia monooxygenase subunit A (amoA) gene of ammonia-oxidizing archaea (AOA), which plays a crucial part in the nitrification process, is such a gene. By providing a full overview of the community of a functional microbial guild, 16S ribosomal ribonucleic acid (rRNA) gene sequencing could overcome this problem. However, it remains unclear how 16S rRNA primer selection influences the quantification of relative abundance and the identification of community composition of nitrifiers, especially AOA. In the present study, a comparison was made between the performance of primer pairs 338F-806R, 515F-806R, and 515F-907R to a shotgun metagenome approach. The structure of nitrifier communities subjected to different long-term organic matter amendment and water management protocols was assessed. Overall, we observed higher Chao1 richness diversity of soil total bacteria by using 515F-806R compared to 338F-806R and 515F-907R, while higher Pielou's evenness diversity was observed by using 515F-806R and 515F-907R compared to 338F-806R. The studied primer pairs revealed different performances on the relative abundance of Thaumarchaeota, AOB, and NOB. The Thaumarchaeota 16S rRNA sequence was rarely detected using 338F-806R, while the relative abundances of Thaumarchaeota detected using 515F-806R were higher than those detected by using 515F-907R. AOB showed higher proportions in the 338F-806R and 515F-907R data, than in 515F-806R data. Different primers pairs showed significant change in relative proportion of NOB. Nonetheless, we found consistent patterns of the phylotype distribution of nitrifiers in different treatments. Nitrosopumilales (NP) and Nitrososphaerales (NS) clades were the dominant members of the AOA community in soils subject to controlled irrigation, whereas Ca. Nitrosotaleales (NT) and NS clades dominated the AOA community in soils subject to flooding irrigation. Nitrospira lineage II was the dominant NOB phylotype in all samples. Overall, ideal 16S rRNA primer pairs were identified for the analysis of nitrifier communities. Moreover, NP and NT clades of AOA might have distinct environmental adaptation strategies under different irrigation treatments.

Green Roof Substrate Microbes Compose a Core Community of Stress-Tolerant Taxa.

Extensive green roofs provide for many ecosystem services in urban environments. The efficacy of these services is influenced by the vegetation structure. Despite their key role in plant performance and productivity, but also their contribution to nitrogen fixation or carbon sequestration, green roof microbial communities have received little attention so far. No study included a spatiotemporal aspect to investigate the core microbiota residing in the substrates of extensive green roofs, although these key taxa are hypothesized to be amongst the most ecologically important taxa. Here, we identified the core microbiota residing in extensive green roof substrates and investigated whether microbial community composition is affected by the vegetation that is planted on extensive green roofs. Eleven green roofs from three different cities in Flanders (Belgium), planted either with a mixture of grasses, wildflowers and succulents (Sedum spp.; Sedum-herbs-grasses roofs) or solely species of Sedum (Sedum-moss roofs), were seasonally sampled to investigate prokaryotic and fungal communities via metabarcoding. Identifying the key microbial taxa revealed that most taxa are dominant phylotypes in soils worldwide. Many bacterial core taxa are capable of nitrogen fixation, and most fungal key taxa are stress-tolerant saprotrophs, endophytes, or both. Considering that soil microbes adapted to the local edaphic conditions have been found to improve plant fitness, further investigation of the core microbiome is warranted to determine the extent to which these stress-tolerant microbes are beneficial for the vegetational layer. Although Sedum-herbs-grasses roofs contained more plant species than Sedum-moss roofs, we observed no discriminant microbial communities between both roof types, likely due to sharing the same substrate textures and the vegetational layers that became more similar throughout time. Future studies are recommended to comprehensively characterize the vegetational layer and composition to examine the primary drivers of microbial community assembly processes.

Microbiota and Long-Term Prognosis in Liver Cirrhosis

Purpose. To compare the gut microbiota in patients with an anamnesis of liver cirrhosis of less than and more than 10 years. Materials and methods. A one-stage study and metagenomic fecal sequencing of 40 hospitalized patients with liver cirrhosis were conducted, of which 35 were with a history of cirrhosis of less than 10 years and 5 — more than 10 years. High-throughput sequencing was performed using a MiSeq genetic analyzer (Illumina, USA) and a protocol based on analysis of 16s rRNA gene variable regions. The study was registered in Clinicaltrials.gov (NCT05335213). Data analysis was performed using Kraken2 algorithm. The analysis of the difference in the proportional composition of the microbiome between the groups was carried out using polynomial Dirichlet modeling (Likelihood-Ratio-Test Statistics: Several Sample Dirichlet-Multinomial Test Comparison), the Mann-Whitney test with preliminary data transformation by CLR transformation (Centered log ratio transform), differential analysis of gene expression based on negative binomial distribution (DESeq2). The significance level α assumed to be 0.05. Results. In patients with liver cirrhosis, the dominant phylotypes of fecal microbiota are Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, minor components include taxa Aquificae, Coprothermobacterota, Tenericutes, Verrucomicrobia, Chloroflexi, Deinococcus-Thermus, Thermotogae, Chlorobi. Significant differences have been established in the density of dominant and minor philotypes of gut bacteria, such as Actinobacteria, Proteobacteria, Tenericutes, Coprothermobacterota, as well as some classes, genera, bacterial species in patients with different disease duration (p &lt; 0.05). Conclusion. There is no doubt about the effect of gut microbiota on compensation for liver function. The established differences in the composition of the microbiota in patients with liver cirrhosis depending on survival over 10 years are of scientific and practical importance for the formation of an evidence-based approach to the use of microbiome-associated interventions

Tibetan Plateau grasslands might increase sequestration of microbial necromass carbon under future warming

Microbial necromass carbon (MNC) can reflect soil carbon (C) sequestration capacity. However, changes in the reserves of MNC in response to warming in alpine grasslands across the Tibetan Plateau are currently unclear. Based on large-scale sampling and published observations, we divided eco-clusters based on dominant phylotypes, calculated their relative abundance, and found that their averaged importance to MNC was higher than most other environmental variables. With a deep learning model based on stacked autoencoder, we proved that using eco-cluster relative abundance as the input variable of the model can accurately predict the overall distribution of MNC under current and warming conditions. It implied that warming could lead to an overall increase in the MNC in grassland topsoil across the Tibetan Plateau, with an average increase of 7.49 mg/g, a 68.3% increase. Collectively, this study concludes that alpine grassland has the tendency to increase soil C sequestration capacity on the Tibetan Plateau under future warming.

Anthropogenic contamination sources drive differences in antimicrobial-resistant Escherichia coli in three urban lakes.

Antimicrobial resistance (AMR) is an ever-present threat to the treatment of infectious diseases. However, the potential relevance of this phenomenon in environmental reservoirs still raises many questions. Detection of antimicrobial-resistant bacteria in the environment is a critical aspect for understanding the prevalence of resistance outside of clinical settings, as detection in the environment indicates that resistance is likely already widespread. We isolated antimicrobial-resistant Escherichia coli from three urban waterbodies over a 15-month time series, determined their antimicrobial susceptibilities, investigated their population structure, and identified genetic determinants of resistance. We found that E. coli populations at each site were composed of different dominant phylotypes and showed distinct patterns of antimicrobial and multidrug resistance, despite close geographic proximity. Many strains that were genome-sequenced belonged to sequence types of international concern, particularly the ST131 clonal complex. We found widespread resistance to clinically important antimicrobials such as amoxicillin, cefotaxime, and ciprofloxacin, but found that all strains were susceptible to amikacin and the last-line antimicrobials meropenem and fosfomycin. Resistance was most often due to acquirable antimicrobial resistance genes, while chromosomal mutations in gyrA, parC, and parE conferred resistance to quinolones. Whole-genome analysis of a subset of strains further revealed the diversity of the population of E. coli present, with a wide array of AMR and virulence genes identified, many of which were present on the chromosome, including blaCTX-M. Finally, we determined that environmental persistence, transmission between sites, most likely mediated by wild birds, and transfer of mobile genetic elements likely contributed significantly to the patterns observed.IMPORTANCEA One Health perspective is crucial to understand the extent of antimicrobial resistance (AMR) globally, and investigation of AMR in the environment has been increasing in recent years. However, most studies have focused on waterways that are directly polluted by sewage, industrial manufacturing, or agricultural activities. Therefore, there remains a lack of knowledge about more natural, less overtly impacted environments. Through phenotypic and genotypic investigation of AMR in Escherichia coli, this study adds to our understanding of the extent and patterns of resistance in these types of environments, including over a time series, and showed that complex biotic and abiotic factors contribute to the patterns observed. Our study further emphasizes the importance of incorporating the surveillance of microbes in freshwater environments in order to better comprehend potential risks for both human and animal health and how the environment may serve as a sentinel for potential future clinical infections.

Salinity changes the nitrification activity and community composition of comammox Nitrospira in intertidal sediments of Yangtze River estuary.

The newly discovered complete ammonia-oxidizing (comammox) Nitrospira has been identified in different environments, including coastal environments, where salinity is one of the most important factors for the abundance and activity of nitrifiers. Here, we demonstrate the effect of salinity on comammox Nitrospira, canonical ammonia-oxidizing bacteria (AOB), and ammonia-oxidizing archaea (AOA) in the intertidal sediments of the Yangtze River estuary based on microcosm experiments, DNA stable-isotope probing (DNA-SIP), and potential ammonium-oxidation rate (PAR) tests for different groups of ammonia oxidizers with selective inhibitors. During microcosm incubations, the abundance of comammox Nitrospira was more sensitive to increased salinity than that of other ammonia oxidizers. The results obtained with DNA-SIP heavy fractions showed that the dominant phylotype in clade A.2 (containing genes involved in the adaptation to haloalkaline environments) had high proportions in comammox Nitrospira community under both freshwater (0.06% salinity) and highly saline water (3% salinity) conditions. In contrast, another phylotype of clade A.2 (which lacks these genes) was dominant only under freshwater conditions. The PARs confirmed that comammox Nitrospira presented greater contributions to nitrification under freshwater conditions with a PAR of 4.37 ± 0.53 mg N·day-1·kg soil-1 (54%) than under saline water conditions with a PAR of 0.60 ± 0.94 mg N·day-1·kg soil-1 (18%). Moreover, AOA were specific to saline water conditions, whereas AOB were common under both freshwater and saline water conditions (44% and 52%, respectively). The present study provided evidence that salinity markedly affects the activity of comammox Nitrospira, and that the salt sensitivity of different phylotypes varies. IMPORTANCE Complete ammonia oxidation (comammox) is a newly discovered type of nitrification through which ammonia is oxidized to nitrate in an organism. Comammox Nitrospira were abundantly found in coastal ecosystems and demonstrated high community diversity. Changes in salinity are considered one of the most important factors to comammox Nitrospira in coastal ecosystems; however, reports on the correlation between them remain inconsistent. Therefore, it is critical to experimentally determine the influence of salinity on comammox Nitrospira in the coastal ecosystem. This study demonstrated a clear effect of salinity on the abundance, activity, and relative contribution of different ammonia oxidizers, especially for comammox Nitrospira. To the best of our knowledge, this is the first study demonstrating comammox Nitrospira activity at seawater salinities, implying the existence of a salt-tolerant type comammox Nitrospira, despite its activity being much lower than in freshwater conditions. The indicated correlation between the activity of specific comammox Nitrospira and salinity is anticipated to provide insights into the distribution of comammox Nitrospira and their potential contributions in estuaries and coastal ecosystems.

Surface Bacterioplankton Community Structure Crossing the Antarctic Circumpolar Current Fronts.

The Antarctic Circumpolar Current (ACC) is the major current in the Southern Ocean, isolating the warm stratified subtropical waters from the more homogeneous cold polar waters. The ACC flows from west to east around Antarctica and generates an overturning circulation by fostering deep-cold water upwelling and the formation of new water masses, thus affecting the Earth's heat balance and the global distribution of carbon. The ACC is characterized by several water mass boundaries or fronts, known as the Subtropical Front (STF), Subantarctic Front (SAF), Polar Front (PF), and South Antarctic Circumpolar Current Front (SACCF), identified by typical physical and chemical properties. While the physical characteristics of these fronts have been characterized, there is still poor information regarding the microbial diversity of this area. Here we present the surface water bacterioplankton community structure based on 16S rRNA sequencing from 13 stations sampled in 2017 between New Zealand to the Ross Sea crossing the ACC Fronts. Our results show a distinct succession in the dominant bacterial phylotypes present in the different water masses and suggest a strong role of sea surface temperatures and the availability of Carbon and Nitrogen in controlling community composition. This work represents an important baseline for future studies on the response of Southern Ocean epipelagic microbial communities to climate change.

Ecological Dynamics of Broad- and Narrow-Host-Range Viruses Infecting the Bloom-Forming Toxic Cyanobacterium Microcystis aeruginosa.

Microcystis aeruginosa is predicted to interact and coexist with diverse broad- and narrow-host-range viruses within a bloom; however, little is known about their affects on Microcystis population dynamics. Here, we developed a real-time PCR assay for the quantification of these viruses that have different host ranges. During the sampling period, total Microcystis abundance showed two peaks in May and August with a temporary decrease in June. The Microcystis population is largely divided into three phylotypes based on internal transcribed sequences (ITS; ITS types I to III). ITS I was the dominant phylotype (66% to 88%) except in June. Although the ITS II and III phylotypes were mostly less abundant, these phylotypes temporarily increased to approximately equivalent abundances of the ITS I population in June. During the same sampling period, the abundances of the broad-host-range virus MVGF_NODE331 increased from April to May and from July to October with a temporary decrease in June, in which its dynamics were in proportion to the increase of total Microcystis abundances regardless of changes in host ITS population composition. In contrast, the narrow-host-range viruses MVG_NODE620 and Ma-LMM01 were considerably less abundant than the broad-host-range virus and generally did not fluctuate in the environment. Considering that M. aeruginosa could increase the abundance and sustain the bloom under the prevalence of the broad-host-range virus, host abundant and diverse antiviral mechanisms might contribute to coexistence with its viruses. IMPORTANCE The bloom-forming toxic cyanobacterium Microcystis aeruginosa interacts with diverse broad- and narrow-host-range viruses. However, the dynamics of the Microcystis population (at the intraspecies level) and viruses with different host ranges remain unknown. Our real-time PCR assays unveiled that the broad-host-range virus gradually increased in abundance over the sampling period, in proportion to the increase in total Microcystis abundance regardless of changes in genotypic composition. The narrow-host-range viruses were considerably less abundant than the broad-host-range virus and did not generally fluctuate in the environment. The expansion and maintenance of the Microcystis bloom even under the increased infection by the broad-host-range virus suggested that highly abundant and diverse antiviral mechanisms allowed them to coexist with viruses under selective pressure. This paper expands our knowledge about the ecological dynamics of Microcystis viruses and provides potential insights into their coexistence with their host.

Филогенетическое разнообразие микроорганизмов источника Абаканский Аржан – потенциальных продуцентов микробной энергии

Microbial energy is a promising area of innovative development in bio- and nanotechnology. Recent studies have revealed that microbial communities of thermal springs have excellent implementation prospects in this area. The present article introduces the microbial diversity of the Abakan Arzhan thermal spring and their isolates that are potentially applicable in microbial electricity synthesis. &#x0D; The research featured microbial isolates obtained from a microbiota analysis of water and slit samples from the Abakan Arzhan thermal spring. The study involved a metagenomic analysis of the microbial community, as well as such molecular biology methods as nucleic acid extraction, PCR, sequencing, phylogenetic, and bioinformatic analysis. The Silva library was used to compare 16S RNA sequences&#x0D; Firmicutes, Bacteroides, and Proteobacteria proved to be the dominant phylotypes for water samples, while Firmicutes, Thermomonas, Gammaproteobacteria, and Proteobacteria were the dominant phylotypes for slit samples. The analysis of minor phylotypes confirmed the presence of Geobacter and Shewanella in the samples. The total number of obtained enrichment cultures was nine. Two types of resistant colonies were discovered during the isolation of extremophilic iron-reducing isolates. The samples were grown on a medium containing iron (III) acetate and iron (III) nitrate, and the isolates appeared to be in the process of Fe(III) reduction. The isolates showed an intense iron recovery of 409 and 407 µg/mL after 72 h of cultivation.&#x0D; The study confirmed the ability of the acquired isolates to reduce iron, making them a priority for future microbial energy research. The isolates belonged to the Shewanella algae and Geobacter sulfurreducens species, as determined by 16S RNA morphology and phylogenetic analyses.

Microbiome Restructuring: Dominant Coral Bacterium Endozoicomonas Species Respond Differentially to Environmental Changes.

ABSTRACTBacteria in the coral microbiome play a crucial role in determining coral health and fitness, and the coral host often restructures its microbiome composition in response to external factors. An important but often neglected factor determining this microbiome restructuring is the ability of microbiome members to respond to changes in the environment. To address this issue, we examined how the microbiome structure of Acropora muricata corals changed over 9 months following a reciprocal transplant experiment. Using a combination of metabarcoding, genomics, and comparative genomics approaches, we found that coral colonies separated by a small distance harbored different dominant Endozoicomonas-related phylotypes belonging to two different species, including a novel species, “Candidatus Endozoicomonas penghunesis” 4G, whose chromosome-level (complete) genome was also sequenced in this study. Furthermore, the two dominant Endozoicomonas species had different potentials to scavenge reactive oxygen species, suggesting potential differences in responding to the environment. Differential capabilities of dominant members of the microbiome to respond to environmental change can (i) provide distinct advantages or disadvantages to coral hosts when subjected to changing environmental conditions and (ii) have positive or negative implications for future reefs.IMPORTANCE The coral microbiome has been known to play a crucial role in host health. In recent years, we have known that the coral microbiome changes in response to external stressors and that coral hosts structure their microbiome in a host-specific manner. However, an important internal factor, the ability of microbiome members to respond to change, has been often neglected. In this study, we combine metabarcoding, culturing, and genomics to delineate the differential ability of two dominant Endozoicomonas species, including a novel “Ca. Endozoicomonas penghunesis” 4G, to respond to change in the environment following a reciprocal transplant experiment.

Bacterial and archaeal communities in saline soils from a Los Negritos geothermal area in Mexico

In recent years, there has been a growing need to understand how salinity affects microbial communities in agricultural soils. The archaeal and bacterial community diversity and structure were investigated through high-throughput sequencing analysis of their 16S rRNA in two arable soils with low electrolytic conductivity (EC) (arable 1 soil 2.3 dS m -1 and arable 2 soil 2.6 dS m -1 ) and a saline soil (EC = 17.6 dS m -1 ). The dominant bacterial phyla in the soils were Proteobacteria (relative abundance 46.2±8.9%), followed by Acidobacteria (13.1±9.1%) and Actinobacteria (10.0±4.8%), while Serratia (6.0±5.8%) and Bacillus (4.0±3.6%) were the dominant bacterial genera. Candidatus Nitrososphaera (53.5±46.8%) was the dominant archaeal phylotype in the arable soils, whereas Nitrosopumilus (0.4±0.01%) in the saline soil. The archaeal and bacterial community structure was different between the soils and the sand, As, Ba and Sb content had a significant effect on bacterial and archaeal community structure in the soils of this study, but not soil salinity.

Amplicon-Based Analysis of the Fungal Diversity across Four Kenyan Soda Lakes.

Microorganisms have been able to colonize and thrive in extreme environments characterized by low/high pH, temperature, salt, or pressure. Examples of extreme environments are soda lakes and soda deserts. The objective of this study was to explore the fungal diversity across soda lakes Magadi, Elmenteita, Sonachi, and Bogoria in Kenya. A new set of PCR primers was designed to amplify a fragment long enough for the 454-pyrosequencing technology. Analysis of the amplicons generated showed that the new primers amplified for diverse fungal groups. A total of 153,634 quality-filtered, nonchimeric sequences derived from the 18S region of the rRNA region were used for community diversity analysis. The sequence reads were clustered into 502 OTUs at 97% similarity cut-off using BLASTn analysis of which 432 were affiliated to known fungal phylotypes and the rest to other eukaryotes. Fungal OTUs were distributed across 107 genera affiliated to the phyla Ascomycota, Basidiomycota, Glomeromycota, and and other unclassified groups refred to as Incertae sedis. The phylum Ascomycota was the most abundant in terms of OTUs. Overall, fifteen genera (Chaetomium, Monodictys, Arthrinium, Cladosporium, Fusarium, Myrothecium, Phyllosticta, Coniochaeta, Diatrype, Sarocladium, Sclerotinia, Aspergillus, Preussia, and Eutypa) accounted for 65.3% of all the reads. The genus Cladosporium was detected across all the samples at varying percentages with the highest being water from Lake Bogoria (51.4%). Good's coverage estimator values ranged between 97 and 100%, an indication that the dominant phylotypes were represented in the data. These results provide useful insights that can guide cultivation-dependent studies to understand the physiology and biochemistry of the as-yet uncultured taxa.

Novel application of aerobic granular biofilm systems for treating nitrate-polluted groundwater at low temperature: Microbial community and performance

An aerobic granular biofilm process was operated in a sequential batch reactor for treating nitrate-pollute groundwater at 6 ºC, which was fed with a progressively reduced carbon concentration to understand the nitrate removal efficacy in cold regions by denitrifying microorganisms. The evaluation of the performance reflected a quick granulation promoted by hydraulic stress and a high organic loading rate (OLR). The granules were dense and compact and kept stable conformation until the end of operation, despite the low temperature. Nitrate removal in the stage with high OLR was close to 100%, while the stage with the lowest OLR reached efficiencies higher than 87% in steady-state, suppose a successful advantage against other biological processes for treating drinking water. The bacterial community in the mature granules were colonized by cold-adapted microorganisms such as Holophagaceae and Candidatus Microthrix. Methanospirillum and Bathyarchaeota were the most abundant archaeal phylotypes, which showed a more stable consortium and Nectriaceae and Trichosporonaceae were the most dominant fungal phylotypes for all stages. The qPCR revealed that the crucial role was played by Fungi and Bacteria, while Archaea lost abundance in granular biomass, despite extreme conditions. Aerobic granular sludge is a robust biological technology able to remove nitrate in oligotrophic waters bodies.

Polar soils exhibit distinct patterns in microbial diversity and dominant phylotypes

The polar regions, comprising the Antarctic, Arctic and Tibetan Plateau, represent the most extreme environments on Earth. Soils across the polar regions harbor diverse microorganisms, which dominate the biogeochemical cycling. However, polar soil microbial diversity is largely underrepresented, and has not been directly compared with the non-polar regions at a global scale, which hinders our understanding of the potential importance of polar microbial diversity. In this study, we investigated the global microbial diversity and taxonomy by comparing 1114 soils, derived from the Antarctic (203), Arctic (432), Tibetan Plateau (104) and non-polar regions (375) across all continents. Soil microbial diversity was found to increase gradually from the Antarctic < Arctic < Tibetan Plateau and < non-polar regions. Soil microbial diversity dominantly corresponded to mean summer temperature in the polar regions and to soil pH in non-polar regions, respectively. Soil microbial community structure significantly differed across the different biogeographical regions, while the Antarctic exhibited the highest habitat-specificity. Over 26,000 phylotypes were observed across global soils, of which 21.8% were unique to the three poles, and 21.2% were apparently ubiquitous globally. Polar soils were dominated by fewer phylotypes, but individual phylotype showed greater dominance than that in non-polar regions. Our study reveals unique patterns of soil microbial diversity and taxonomic compositions in polar regions, and highlights the importance of environmental stresses in controlling soil microbial community.

Analysis of bacterial communities of three cassava-based traditionally fermented Nigerian foods (abacha, fufu and garri).

Globally, cassava is an important food crop that contributes significantly to food security. In Nigeria, cassava can be traditionally processed into abacha (fermented strips), fufu (submerged-fermented porridge) and garri (solid-state fermented farinated granules) for human consumption. Despite the widespread consumption of these foods, there is a major knowledge gap in understanding their core bacterial diversity. This study, therefore, applied next-generation sequencing of 16S rRNA gene to delineate the bacterial diversity in abacha, fufu and garri. Amplicon sequence variants belonging to nine phyla were present in the three foods. Firmicutes dominated the bacterial community of abacha and fufu, whereas, Proteobacteria was the dominant phylum in garri. At genus level taxa, Lactococcus, Lysinibacillus and Pseudomonas dominated the bacterial community in abacha, fufu and garri, respectively. Other dominant phylotypes reported in the foods belonged to Bacillus, Clostridium sensu stricto (cluster 1), Cupriavidus, Enterobacter, Sphingomonas and Staphylococcus. To the best of our knowledge, Clostridium sensu stricto cluster 1 and Lysinibacillus in fufu, and Brevundimonas, Cupriavidus, Sphingomonas and Strenotrophomomas in garri are reported for the first time. Although some potential pathogenic genera were recorded, the foods contained potentially functional species that could be explored to improve artisanal food production, food security and safeguard consumer health.

Composition and potential functional roles of soil fungal communities on arid farms in Arequipa (Southern Peru) characterized using SMRT sequencing

Small farms near Arequipa, Peru face many challenges including crop diseases caused by soil-borne fungal pathogens. Identifying fungi in these soils and factors that shift the balance between pathogenic and beneficial lifestyles will aid in the development of more effective and sustainable disease control strategies. In this study, the composition and potential functional roles of soil fungal communities on 12 farms was characterized using SMRT sequencing. Communities were compared with soil physiochemical properties and farms grouped based on location (River vs. Canal), and farm age (Old, New, Very New) to investigate possible drivers of community structure and function. Communities were dominated by the Ascomycota phylum, and Fusarium, Alternaria and Cladosporium genera. The majority of phylotypes were saprotrophs, however, an unusually large fraction were pathotrophs (14-29%), and 10% of the entire community were plant pathogens. There were correlations between saprophytic and pathogenic phylotypes with soil pH, organic matter, nitrogen and phosphorous, though the strongest driver of community structure were cobalt and nickel. Dominant pathogenic phylotypes in river and canal farms differed indicating the need for more site-specific intervention strategies. Age was positively correlated with a decline in saprotrophs and increase in pathotrophs highlighting the need to replenish soil organic matter. Correlations between individual phylotypes could mediate disease outbreaks and should be explored in future studies. Results of this study confirm that soils in this unique agroecosystem are highly conducive to the survival of soil-borne pathogens, though it should be possible to suppress these organisms via more targeted soil management practices.

The ubiquitous soil verrucomicrobial clade 'Candidatus Udaeobacter' shows preferences for acidic pH.

Members of the verrucomicrobial clade 'Candidatus Udaeobacter' rank among the most dominant bacterial phylotypes in soil. Nevertheless, despite this global prevalence, in-depth analyses with respect to pH preferences of 'Ca. Udaeobacter' representatives are still lacking. Here, we utilized a recently designed primer pair, specifically targeting 'Ca. Udaeobacter', to investigate links between soil pH and the abundance as well as phylotype composition of this largely unexplored verrucomicrobial clade. Based on 150 forest and 150 grassland soils, comprising a broad pH range, we determined the highest total abundance of 'Ca. Udaeobacter' in strongly acidic soil (pH, ~5.1) and, noteworthy, in ultra-acidic soil (pH< 3.5) and at a pH≥ 7, its abundance drastically declined. When we analysed the six most dominant amplicon sequence variants affiliated with 'Ca. Udaeobacter' separately, their abundances peaked within a pH range of approximately 4.7-5.2, and only in one case at slightly acidic soil pH (pH, 6.1). Our study benefits from a combination of quantitative real-time PCR and high-throughput amplicon sequencing, enabling for the first time a highly specific abundance analysis of representatives affiliated with 'Ca. Udaeobacter', which revealed that this globally abundant verrucomicrobial clade shows preferences for acidic soil.

Identification of the phylotypes involved in cis-dichloroethene and 1,4-dioxane biodegradation in soil microcosms

Co-contamination with chlorinated compounds and 1,4-dioxane has been reported at many sites. Recently, there has been an increased interest in bioremediation because of the potential to degrade multiple contaminants concurrently. Towards improving bioremediation efficacy, the current study examined laboratory microcosms (inoculated separately with two soils) to determine the phylotypes and functional genes associated with the biodegradation of two common co-contaminants (cis-dichloroethene [cDCE] and 1,4-dioxane). The impact of amending microcosms with lactate on cDCE and 1,4-dioxane biodegradation was also investigated. The presence of either lactate or cDCE did not impact 1,4-dioxane biodegradation one of the two soils. Lactate appeared to improve the initiation of the biological removal of cDCE in microcosms inoculated with either soil. Stable isotope probing (SIP) was then used to determine which phylotypes were actively involved in carbon uptake from cDCE and 1,4-dioxane in both soil communities. The most enriched phylotypes for 13C assimilation from 1,4-dioxane included Rhodopseudomonas and Rhodanobacter. Propane monooxygenase was predicted (by PICRUSt2) to be dominant in the 1,4-dioxane amended microbial communities and propane monooxygenase gene abundance values correlated with other enriched (but less abundant) phylotypes for 13C-1,4-dioxane assimilation. The dominant enriched phylotypes for 13C assimilation from cDCE included Bacteriovorax, Pseudomonas and Sphingomonas. In the cDCE amended soil microcosms, PICRUSt2 predicted the presence of DNA encoding glutathione S-transferase (a known cDCE upregulated enzyme). Overall, the work demonstrated concurrent removal of cDCE and 1,4-dioxane by indigenous soil microbial communities and the enhancement of cDCE removal by lactate. The data generated on the phylotypes responsible for carbon uptake (as determined by SIP) could be incorporated into diagnostic molecular methods for site characterization. The results suggest concurrent biodegradation of cDCE and 1,4-dioxane should be considered for chlorinated solvent site remediation.