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1.
Int J Hyg Environ Health ; 237: 113836, 2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-34481208

RESUMO

Our surrounding environment has been influenced by the COVID-19 pandemic situation. The second wave of COVID-19 in India has proven to be more devastating and aggressive than the first wave of the pandemic, which led to recognizing India as one of the world's topmost worst-hit nations considering >4000 fatalities reported in a single day in May 2021. Such "resurgence and acceleration" of COVID-19 transmission has been fuelled by the MahaKumbh festival and political mass gathering (elections rallies) events, where the COVID-19 protocols have been ignored by millions of pilgrims/followers. The present review discusses only the consequences of this year's MahaKumbh festivals, the largest religious mass gathering on earth, which was held during the COVID-19 pandemic in India, and its impact on both the spread of SARS-CoV-2 among participants and their families and its influence on the quality of the river Ganga. This article tries to give readers outside of India an overview of how much impact of any such single large gathering of any relgion in any part of the world can drive coronavirus infections and effectively commence the second/third wave outbreak with this case study. Furthermore, the religious large scale celebration are widely accepted through out the world that have played a significant role in the spread of the pandemic into remote villages and towns all over the subcontinent/world, thus affecting many areas with insufficient healthcare facilities that have been relatively spared. This review also highlights the potential risk of transmission from infected humans into the aquatic environment of the river Ganga. Besides the obvious relevance of SARS-CoV-2, a large variety of other water-related disease vectors (bacteria, viruses, and protozoa) stemming from visitors to the religious congregation were introduced into the upstream regions of the Ganga river. Their sheer number is assumed to have had a severe influence on its delicate ecosystem, including endangered mammals such as the river Dolphins. The detailed epidemiological and clinical study on transmission routes of SARS-CoV-2 is the need of the hour to understand the pathogenesis of RNA virus infection and prevent the massive spreading of such infectious respiratory diseases. An interdisciplinary approach, rooted in evidence-based efficient learning, contextual strategies, and a streamlined unified approach should be adopted to help in the development of a proactive prevention model during future MahaKumbh festival (and similar religious gatherings) instead of just "picking up the pieces" in a conventional post-event model.


Assuntos
COVID-19/transmissão , Férias e Feriados , Rios/microbiologia , SARS-CoV-2 , Animais , Espécies em Perigo de Extinção , Humanos , Índia , Microbiologia da Água , Poluição da Água
2.
Appl Environ Microbiol ; 87(20): e0133921, 2021 09 28.
Artigo em Inglês | MEDLINE | ID: mdl-34347514

RESUMO

Permafrost soils store approximately twice the amount of carbon currently present in Earth's atmosphere and are acutely impacted by climate change due to the polar amplification of increasing global temperature. Many organic-rich permafrost sediments are located on large river floodplains, where river channel migration periodically erodes and redeposits the upper tens of meters of sediment. Channel migration exerts a first-order control on the geographic distribution of permafrost and floodplain stratigraphy and thus may affect microbial habitats. To examine how river channel migration in discontinuous permafrost environments affects microbial community composition, we used amplicon sequencing of the 16S rRNA gene on sediment samples from floodplain cores and exposed riverbanks along the Koyukuk River, a large tributary of the Yukon River in west-central Alaska. Microbial communities are sensitive to permafrost thaw: communities found in deep samples thawed by the river closely resembled near-surface active-layer communities in nonmetric multidimensional scaling analyses but did not resemble floodplain permafrost communities at the same depth. Microbial communities also displayed lower diversity and evenness in permafrost than in both the active layer and permafrost-free point bars recently deposited by river channel migration. Taxonomic assignments based on 16S and quantitative PCR for the methyl coenzyme M reductase functional gene demonstrated that methanogens and methanotrophs are abundant in older permafrost-bearing deposits but not in younger, nonpermafrost point bar deposits. The results suggested that river migration, which regulates the distribution of permafrost, also modulates the distribution of microbes potentially capable of producing and consuming methane on the Koyukuk River floodplain. IMPORTANCE Arctic lowlands contain large quantities of soil organic carbon that is currently sequestered in permafrost. With rising temperatures, permafrost thaw may allow this carbon to be consumed by microbial communities and released to the atmosphere as carbon dioxide or methane. We used gene sequencing to determine the microbial communities present in the floodplain of a river running through discontinuous permafrost. We found that the river's lateral movement across its floodplain influences the occurrence of certain microbial communities-in particular, methane-cycling microbes were present on the older, permafrost-bearing eroding riverbank but absent on the newly deposited river bars. Riverbank sediment had microbial communities more similar to those of the floodplain active-layer samples than permafrost samples from the same depth. Therefore, spatial patterns of river migration influence the distribution of microbial taxa relevant to the warming Arctic climate.


Assuntos
Microbiota , Pergelissolo/microbiologia , Rios/microbiologia , Alaska , Ciclo do Carbono , Movimentos da Água
3.
J Forensic Sci ; 66(6): 2307-2318, 2021 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-34462924

RESUMO

Death investigations in aquatic ecosystems are challenging due to abiotic and biotic factors that may influence the estimation of a postmortem submersion interval (PMSI). In this study, we examined bacterial changes throughout the decomposition process on porcine carcasses submerged in a tidal-influenced river and identified predictors of epinecrotic community succession. Fetal porcine (Sus scrofa) carcasses (N = 6) were submerged with epinecrotic samples collected every 3 days (6 collections) over a period of 19 days (~7415 accumulated degree hours (ADH)). Amplicon sequencing was performed using the Illumina MiSeq platform (16S V4 region, 2 × 250 bp format) to identify changes in bacterial relative abundance and diversity. To match bacterial succession with rough taphonomy, carcasses were visually assessed at each sampling time point to determine the decomposition stage. Notably, the three most abundant families were Moraxellaceae, Burkholderiaceae (Proteobacteria), and Clostridiaceae (Firmicutes), though communities composition varied significantly across decomposition stages. Greater bacterial phylogenetic diversity was observed in in latter decomposition stages (advanced floating decay, sunken remains). Random Forest Models were built to predict ADH and explained 77%-80.8% of variation in ADH with an error rate of +/-1943.2 ADH (Root Mean Square Error) or approx. ±2.7 days at the mean water temperature of this study. This study provided a useful model that could be used to estimate a PMSI in this river system utilizing bacterial community succession, and thus, potentially improve the accuracy of such estimations to be used in the court of law.


Assuntos
Restos Mortais , Imersão , Microbiota , Mudanças Depois da Morte , Rios/microbiologia , Animais , DNA Bacteriano/análise , Medicina Legal , Sequenciamento de Nucleotídeos em Larga Escala , Modelos Animais , Filogenia , Suínos
4.
Artigo em Inglês | MEDLINE | ID: mdl-34242155

RESUMO

Cells of strains P66T, V1 and W15Feb18 are Gram-stain-negative short rods and motile by one polar flagellum. Strain P66T was isolated from rainbow trout (Oncorhynchus mykiss) cultivated at a fish farm in Turkey. Strain V1 was isolated from sand of an intertidal shore on the Galicia coast in Spain and strain W15Feb18 was isolated from water collected at the Woluwe River in Belgium. Based on 16S rRNA sequence similarity values, the strains were grouped under the genus Pseudomonas and the Pseudomonas putida phylogenetic group of species. The DNA G+C content ranged from 58.5 to 58.9 mol%. The strains were characterized phenotypically by the API 20NE and Biolog GEN III tests, and chemotaxonomically by their whole-cell MALDI-TOF MS protein profiles and fatty acid contents. The absence of the hydrolysis of gelatin and the assimilation of arabinose, mannose and mannitol differentiated these strains from the closest species, Pseudomonas alkylphenolica. The major fatty acid components were C16:0 (29.91-31.68 %) and summed feature 3 (36.44-37.55 %). Multilocus sequence analysis with four and 83 housekeeping gene sequences and a core proteome analysis showed that these strains formed a phylogenetic cluster in the P. putida group of species. Genome comparisons by the average nucleotide identity based on blast and the Genome-to-Genome Distance Calculator demonstrated that the three strains belonged to the same genomic species and were distant from any known species, with similarity values lower than the thresholds established for species in the genus Pseudomonas. These data permitted us to conclude that strains P66T, V1 and W15Feb18 belong to a novel species in the genus Pseudomonas, for which the name Pseudomonas arcuscaelestis sp. nov. is proposed. The type strain is P66T (=CECT 30176T=CCUG 74872T). The other strains have been deposited in the CECT with the corresponding collection numbers: V1 (=CECT 30356) and W15Feb18 (=CECT 30355).


Assuntos
Oncorhynchus mykiss/microbiologia , Filogenia , Pseudomonas/classificação , Rios/microbiologia , Microbiologia da Água , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , Bélgica , DNA Bacteriano/genética , Ácidos Graxos/química , Genes Bacterianos , Tipagem de Sequências Multilocus , Hibridização de Ácido Nucleico , Pseudomonas/isolamento & purificação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Espanha , Turquia
5.
Syst Appl Microbiol ; 44(5): 126233, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34311149

RESUMO

Bacteria in the family Geobacteraceae have been proven to fill important niches in a diversity of anaerobic environments and global biogeochemical processes. Here, three bacterial strains in this family, designated Red875T, Red259T, and Red421T were isolated from river sediment and paddy soils in Japan. All of them are Gram-staining-negative, strictly anaerobic, motile, flagellum-harboring cells that form red colonies on agar plates and are capable of utilizing Fe(III)-NTA, Fe(III) citrate, ferrihydrite, MnO2, fumarate, and nitrate as electron acceptors with acetate, propionate, pyruvate, and glucose as electron donors. Phylogenetic analysis based on the 16S rRNA gene and 92 concatenated core proteins sequences revealed that strains Red259T and Red421T clustered with the type strains of Geomonas species, whereas strain Red875T formed an independent lineage within the family Geobacteraceae. Genome comparison based on  average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values clearly distinguished these three strains from other Geobacteraceae members, with lower values than the thresholds for species delineation. Moreover, strain Red875T also shared low average amino acid identity (AAI) and percentage of conserved proteins (POCP) values with the type species of the family Geobacteraceae. Based on these physiological, chemotaxonomic, and phylogenetic distinctions, we propose that strain Red875T (=NBRC 114290T = MCCC 1K04407T) represents a novel genus in the family Geobacteraceae, namely, Geomesophilobacter sediminis gen. nov., sp. nov., and strains Red259T (=NBRC 114288T = MCCC 1K05016T) and Red421T (=NBRC 114289T = MCCC 1K06216T) represent two novel independent species in the genus Geomonas, namely, Geomonas propionica sp. nov. and Geomonas anaerohicana sp. nov., respectively.


Assuntos
Deltaproteobacteria/classificação , Sedimentos Geológicos/microbiologia , Filogenia , Rios/microbiologia , Microbiologia do Solo , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Deltaproteobacteria/isolamento & purificação , Compostos Férricos , Japão , Compostos de Manganês , Óxidos , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
6.
Sci Rep ; 11(1): 14679, 2021 07 19.
Artigo em Inglês | MEDLINE | ID: mdl-34282205

RESUMO

Escherichia coli dynamics in urban watersheds are affected by a complex balance among external inputs, niche modulation and genetic variability. To explore the ecological processes influencing E. coli spatial patterns, we analyzed its abundance and phylogenetic structure in water samples from a stream network with heterogeneous urban infrastructure and environmental conditions. Our results showed that environmental and infrastructure variables, such as macrophyte coverage, DIN and sewerage density, mostly explained E. coli abundance. Moreover, main generalist phylogroups A and B1 were found in high proportion, which, together with an observed negative relationship between E. coli abundance and phylogroup diversity, suggests that their dominance might be due to competitive exclusion. Lower frequency phylogroups were associated with sites of higher ecological disturbance, mainly involving simplified habitats, higher drainage infrastructure and septic tank density. In addition to the strong negative relationship between phylogroup diversity and dominance, the occurrence of these phylogroups would be associated with increased facilitated dispersal. Nutrients also contributed to explaining phylogroup distribution. Our study proposes the differential contribution of distinct ecological processes to the patterns of E. coli in an urban watershed, which is useful for the monitoring and management of fecal pollution.


Assuntos
Escherichia coli/classificação , Rios/microbiologia , Águas Residuárias/microbiologia , Cidades , Ecossistema , Monitoramento Ambiental , Poluição Ambiental , Escherichia coli/genética , Escherichia coli/crescimento & desenvolvimento , Estuários , Microbiota , Filogenia , São Francisco , Microbiologia da Água
7.
Microb Ecol ; 82(2): 365-376, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34219185

RESUMO

The unprecedented COVID-19 pandemic has had major impact on human health worldwide. Whilst national and international COVID-19 lockdown and travel restriction measures have had widespread negative impact on economies and mental health, they may have beneficial effect on the environment, reducing air and water pollution. Mass bathing events (MBE) also known as Kumbh Mela are known to cause perturbations of the ecosystem affecting resilient bacterial populations within water of rivers in India. Lockdowns and travel restrictions provide a unique opportunity to evaluate the impact of minimum anthropogenic activity on the river water ecosystem and changes in bacterial populations including antibiotic-resistant strains. We performed a spatiotemporal meta-analysis of bacterial communities of the Godavari River, India. Targeted metagenomics revealed a 0.87-fold increase in the bacterial diversity during the restricted activity of lockdown. A significant increase in the resilient phyla, viz. Proteobacteria (70.6%), Bacteroidetes (22.5%), Verrucomicrobia (1.8%), Actinobacteria (1.2%) and Cyanobacteria (1.1%), was observed. There was minimal incorporation of allochthonous bacterial communities of human origin. Functional profiling using imputed metagenomics showed reduction in infection and drug resistance genes by - 0.71-fold and - 0.64-fold, respectively. These observations may collectively indicate the positive implications of COVID-19 lockdown measures which restrict MBE, allowing restoration of the river ecosystem and minimise the associated public health risk.


Assuntos
Bactérias/isolamento & purificação , Controle de Doenças Transmissíveis/legislação & jurisprudência , Ecossistema , Rios/microbiologia , Bactérias/classificação , COVID-19/epidemiologia , COVID-19/prevenção & controle , Farmacorresistência Bacteriana , Monitoramento Ambiental , Hinduísmo , Atividades Humanas , Índia/epidemiologia , Análise de Componente Principal
8.
Nat Commun ; 12(1): 3700, 2021 06 17.
Artigo em Inglês | MEDLINE | ID: mdl-34140471

RESUMO

The relationship between detritivore diversity and decomposition can provide information on how biogeochemical cycles are affected by ongoing rates of extinction, but such evidence has come mostly from local studies and microcosm experiments. We conducted a globally distributed experiment (38 streams across 23 countries in 6 continents) using standardised methods to test the hypothesis that detritivore diversity enhances litter decomposition in streams, to establish the role of other characteristics of detritivore assemblages (abundance, biomass and body size), and to determine how patterns vary across realms, biomes and climates. We observed a positive relationship between diversity and decomposition, strongest in tropical areas, and a key role of abundance and biomass at higher latitudes. Our results suggest that litter decomposition might be altered by detritivore extinctions, particularly in tropical areas, where detritivore diversity is already relatively low and some environmental stressors particularly prevalent.


Assuntos
Biota , Ecossistema , Rios , Animais , Biodiversidade , Biomassa , Tamanho Corporal , Chironomidae/fisiologia , Clima , Ephemeroptera/fisiologia , Insetos/fisiologia , Folhas de Planta/química , Floresta Úmida , Rios/química , Rios/microbiologia , Rios/parasitologia , Rios/virologia , Clima Tropical , Tundra
9.
PLoS One ; 16(6): e0253233, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34129622

RESUMO

The spatial and temporal distribution of the archaeal community and its driving factors in the sediments of large-scale regulated rivers, especially in rivers with cascade hydropower development rivers, remain poorly understood. Quantitative PCR (qPCR) and Illumina MiSeq sequencing of the 16S rRNA archaeal gene were used to comprehensively investigate the spatiotemporal diversity and structure of archaeal community in the sediments of the Lancang River cascade reservoirs (LRCR). The archaeal abundance ranged from 5.11×104 to 1.03×106 16S rRNA gene copies per gram dry sediment and presented no temporal variation. The richness, diversity, and community structure of the archaeal community illustrated a drastic spatial change. Thaumarchaeota and Euryyarchaeota were the dominant archaeal phyla in the sediments of the cascade rivers, and Bathyarchaeota was also an advantage in the sediments. PICRUSt metabolic inference analysis revealed a growing number of genes associated with xenobiotic metabolism and carbon and nitrogen metabolism in downstream reservoirs, indicating that anthropogenic pollution discharges might act as the dominant selective force to alter the archaeal communities. Nitrate and C/N ratio were found to play important roles in the formation of the archaeal community composition. In addition, the sediment archaeal community structure was also closely related to the age of the cascade reservoir and hydraulic retention time (HRT). This finding indicates that the engineering factors of the reservoir might be the greatest contributor to the archaeal community structure in the LRCR.


Assuntos
Archaea/crescimento & desenvolvimento , Sedimentos Geológicos/microbiologia , Rios/microbiologia , Archaea/genética , Archaea/metabolismo , Archaea/fisiologia , China , DNA Arqueal/genética , Variação Genética/genética , Sequenciamento de Nucleotídeos em Larga Escala , Filogenia , Reação em Cadeia da Polimerase , RNA Ribossômico 16S/genética , Análise Espaço-Temporal
10.
Sci Rep ; 11(1): 13355, 2021 06 25.
Artigo em Inglês | MEDLINE | ID: mdl-34172779

RESUMO

Expansion of various types of water infrastructure is critical to water security in Africa. To date, analysis of adverse disease impacts has focused mainly on large dams. The aim of this study was to examine the effect of both small and large dams on malaria in four river basins in sub-Saharan Africa (i.e., the Limpopo, Omo-Turkana, Volta and Zambezi river basins). The European Commission's Joint Research Center (JRC) Yearly Water Classification History v1.0 data set was used to identify water bodies in each of the basins. Annual malaria incidence data were obtained from the Malaria Atlas Project (MAP) database for the years 2000, 2005, 2010 and 2015. A total of 4907 small dams and 258 large dams in the four basins, with 14.7million people living close (< 5 km) to their reservoirs in 2015, were analysed. The annual number of malaria cases attributable to dams of either size across the four basins was 0.9-1.7 million depending on the year, of which between 77 and 85% was due to small dams. The majority of these cases occur in areas of stable transmission. Malaria incidence per kilometre of reservoir shoreline varied between years but for small dams was typically 2-7 times greater than that for large dams in the same basin. Between 2000 and 2015, the annual malaria incidence showed a broadly declining trend for both large and small dam reservoirs in areas of stable transmission in all four basins. In conclusion, the malaria impact of dams is far greater than previously recognized. Small and large dams represent hotspots of malaria transmission and, as such, should be a critical focus of future disease control efforts.


Assuntos
Malária/transmissão , Água/química , África ao Sul do Saara , Gerenciamento de Dados , Humanos , Incidência , Rios/microbiologia , Abastecimento de Água/métodos
11.
PLoS One ; 16(5): e0250527, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34038450

RESUMO

Slow growing oomycete isolates with morphological resemblance to Phytophthora were obtained from forest streams during routine monitoring for the EU quarantine forest pathogen Phytophthora ramorum in Ireland and Northern Ireland. Internal Transcribed Spacer (ITS) sequence analysis indicated that they belonged to two previously unknown species of Nothophytophthora, a recently erected sister genus of Phytophthora. Morphological and temperature-growth studies were carried out to characterise both new species. In addition, Bayesian and Maximum-Likelihood analyses of nuclear 5-loci and mitochondrial 3-loci datasets were performed to resolve the phylogenetic positions of the two new species. Both species were sterile, formed chlamydospores and partially caducous nonpapillate sporangia, and showed slower growth than any of the six known Nothophytophthora species. In all phylogenetic analyses both species formed distinct, strongly supported clades, closely related to N. chlamydospora and N. valdiviana from Chile. Based on their unique combination of morphological and physiological characters and their distinct phylogenetic positions the two new species are described as Nothophytophthora irlandica sp. nov. and N. lirii sp. nov. Their potential lifestyle and geographic origin are discussed.


Assuntos
DNA Espaçador Ribossômico/genética , Filogenia , Phytophthora/isolamento & purificação , Doenças das Plantas/microbiologia , Rios/microbiologia , Análise de Sequência de DNA/métodos , Estramenópilas/isolamento & purificação , Irlanda do Norte , Phytophthora/genética , Estramenópilas/genética
12.
Arch Microbiol ; 203(6): 3163-3169, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-33821299

RESUMO

In this study, aimed at investigating and characterizing river sediment bacteria, we isolated a Gram-stain-positive, rod-shaped, obligate anaerobic bacterium, strain CBA3637T, from the sediment of the Geum River. This strain grew at 10-40 °C (optimum, 30 °C), 0-1% NaCl (optimum, 0%), and pH 7-8 (optimum, pH 7). The 16S rRNA gene sequence comparison revealed Aminipila butyrica DSM 103574T to be the closest relative of strain CBA3637T (96.6-96.7% similarity); and both strains clustered together in phylogenetic analysis. The genome of strain CBA3637T was found to consist of a single chromosome (3.51 Mbp; 36.98% G + C content). Comparative genomic analysis of the strain CBA3637T with A. butyrica DSM 103574T revealed that strain CBA3637T possessed five unique pathways related to polyamine biosynthesis, lipopolysaccharide metabolism, pyrimidine metabolism, and cofactor and vitamin metabolism. Strain CBA3637T contained C14:0, C16:0, and C18:1 ω9c as the major fatty acids, and diphosphatidylglycerol as the major polar lipid. No respiratory quinone was observed. Biochemical, chemotaxonomic, and genotypic data revealed that the strain CBA3637T is a representative of a novel species within the genus Aminipila, for which the name Aminipila terrae is proposed. The type strain is CBA3637T (= KACC 21651T = DSM 110662T).


Assuntos
Clostridiales , Sedimentos Geológicos , Fosfolipídeos , Rios , Anaerobiose , Composição de Bases , Clostridiales/classificação , Clostridiales/genética , Clostridiales/isolamento & purificação , Ácidos Graxos/análise , Sedimentos Geológicos/microbiologia , Fosfolipídeos/análise , Filogenia , RNA Ribossômico 16S/genética , Rios/microbiologia
13.
Commun Biol ; 4(1): 457, 2021 04 12.
Artigo em Inglês | MEDLINE | ID: mdl-33846529

RESUMO

Aquatic environments are key niches for the emergence, evolution and dissemination of antimicrobial resistance. However, the population diversity and the genetic elements that drive the dynamics of resistant bacteria in different aquatic environments are still largely unknown. The aim of this study was to understand the population genomics and evolutionary events of Escherichia coli resistant to clinically important antibiotics including aminoglycosides, in anthropogenic and natural water ecosystems. Here we show that less different E. coli sequence types (STs) are identified in wastewater than in rivers, albeit more resistant to antibiotics, and with significantly more plasmids/cell (6.36 vs 3.72). However, the genomic diversity within E. coli STs in both aquatic environments is similar. Wastewater environments favor the selection of conserved chromosomal structures associated with diverse flexible plasmids, unraveling promiscuous interplasmidic resistance genes flux. On the contrary, the key driver for river E. coli adaptation is a mutable chromosome along with few plasmid types shared between diverse STs harboring a limited resistance gene content.


Assuntos
Antibacterianos/farmacologia , Farmacorresistência Bacteriana , Escherichia coli/genética , Variação Genética , Genoma Bacteriano , Rios/microbiologia , Águas Residuárias/microbiologia , Metagenômica , Plasmídeos/fisiologia , Espanha
14.
Artigo em Inglês | MEDLINE | ID: mdl-33847556

RESUMO

A novel bacterial strain, EJ-4T, isolated from stream water collected at Seo-ho in Suwon, Republic of Korea, was characterized based on a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain EJ-4T belonged to the genus Comamonas. The isolate is Gram-stain-negative, non-motile, aerobic, rod-shaped and forms pale yellow colonies on trypticase soy agar. The optimal growth of this strain was observed aerobically at 30 °C, pH 7 and 0.5 % NaCl. The major fatty acids were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c; 39.7 %) and C16 : 0 (32.0 %). The G+C content of strain EJ-4T was 58.4mol %. The average nucleotide identity and digital DNA-DNA hybridization values between strain EJ-4T and Comamoas testosteroni were 91.8 and 31.2 %, respectively. The major polar lipids detected in the isolate were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant isoprenoid quinone was ubiquinone-8. Based on the results of polyphasic taxonomic analysis of strain EJ-4T, we describe a novel species of the genus Comamonas, for which the name Comamonas suwonensis sp. nov. has been proposed, with EJ-4T (=KCTC 82074T=JCM 34179T=KEMB 1602-279T) as the type strain.


Assuntos
Comamonas/classificação , Filogenia , Rios/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , Comamonas/isolamento & purificação , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , Pigmentação , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Ubiquinona/química
15.
Artigo em Inglês | MEDLINE | ID: mdl-33881985

RESUMO

A Gram-stain-negative, aerobic, non-motile and rod-shaped bacterium, designated as IMCC34836T, was isolated from a freshwater stream. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain IMCC34836T was most closely related to Permianibacter aggregans HW001T (of the family Pseudomonadaceae) with 95.6 % sequence similarity and formed a robust clade with P. aggregans HW001T. The draft genome sequence of strain IMCC34836T was 4.4 Mbp in size with 59.1 mol% DNA G+C content. Average nucleotide identity and digital DNA-DNA hybridization values between strain IMCC34836T and P. aggregans HW001T were 71.2 and 22.0 %, respectively, indicating that the new strain represents a novel species. The strain contained iso-C15 : 0, summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and summed feature 9 (iso-C17 : 1 ω9c and/or C16 : 1 10-methyl) as the major fatty acids and harboured phosphatidylethanolamine, two unidentified aminophospholipids and three unidentified lipids as major polar lipids. The isoprenoid quinone detected in the strain was ubiquinone-8. Based on the phylogenetic and phenotypic characteristics, strain IMCC34836T is considered to represent a novel species of the genus Permianibacter, for which the name Permianibacter fluminis sp. nov. is proposed. The type strain is IMCC34836T (=KACC 21755T=NBRC 114416T).


Assuntos
Filogenia , Pseudomonadaceae/classificação , Rios/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfatidiletanolaminas , Fosfolipídeos/química , Pseudomonadaceae/isolamento & purificação , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Ubiquinona/química
16.
J Vis Exp ; (170)2021 04 04.
Artigo em Inglês | MEDLINE | ID: mdl-33871451

RESUMO

Hydraulic fracturing (HF), commonly called "fracking", uses a mixture of high-pressure water, sand, and chemicals to fracture rocks, releasing oil and gas. This process revolutionized the U.S. energy industry, as it gives access to resources that were previously unobtainable and now produces two-thirds of the total natural gas in the United States. Although fracking has had a positive impact on the U.S. economy, several studies have highlighted its detrimental environmental effects. Of particular concern is the effect of fracking on headwater streams, which are especially important due to their disproportionately large impact on the health of the entire watershed. The bacteria within those streams can be used as indicators of stream health, as the bacteria present and their abundance in a disturbed stream would be expected to differ from those in an otherwise comparable but undisturbed stream. Therefore, this protocol aims to use the bacterial community to determine if streams have been impacted by fracking. To this end, sediment, and water samples, from streams near fracking (potentially impacted) and upstream or in a different watershed of fracking activity (unimpacted) must be collected. Those samples are then subjected to nucleic acid extraction, library preparation, and sequencing to investigate microbial community composition. Correlational analysis and machine learning models can subsequently be employed to identify which features are explanative of variation in the community, as well as identification of predictive biomarkers for fracking's impact. These methods can reveal a variety of differences in the microbial communities among headwater streams, based on the proximity to fracking, and serve as a foundation for future investigations on the environmental impact of fracking activities.


Assuntos
Bactérias/isolamento & purificação , Fraturamento Hidráulico , Microbiota , Rios/microbiologia , Gás Natural , Microbiologia da Água
17.
PLoS One ; 16(4): e0250401, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33886647

RESUMO

The Rimac river is the main source of water for Lima, Peru's capital megacity. The river is constantly affected by different types of contamination including mine tailings in the Andes and urban sewage in the metropolitan area. In this work, we aim to produce the first characterization of aquatic bacterial communities in the Rimac river using a 16S rRNA metabarcoding approach which would be useful to identify bacterial diversity and potential understudied pathogens. We report a lower diversity in bacterial communities from the Lower Rimac (Metropolitan zone) in comparison to other sub-basins. Samples were generally grouped according to their geographical location. Bacterial classes Alphaproteobacteria, Bacteroidia, Campylobacteria, Fusobacteriia, and Gammaproteobacteria were the most frequent along the river. Arcobacter cryaerophilus (Campylobacteria) was the most frequent species in the Lower Rimac while Flavobacterium succinicans (Bacteroidia) and Hypnocyclicus (Fusobacteriia) were the most predominant in the Upper Rimac. Predicted metabolic functions in the microbiota include bacterial motility and quorum sensing. Additional metabolomic analyses showed the presence of some insecticides and herbicides in the Parac-Upper Rimac and Santa Eulalia-Parac sub-basins. The dominance in the Metropolitan area of Arcobacter cryaerophilus, an emergent pathogen associated with fecal contamination and antibiotic multiresistance, that is not usually reported in traditional microbiological quality assessments, highlights the necessity to apply next-generation sequencing tools to improve pathogen surveillance. We believe that our study will encourage the integration of omics sciences in Peru and its application on current environmental and public health issues.


Assuntos
Organismos Aquáticos/genética , Arcobacter/genética , Código de Barras de DNA Taxonômico/métodos , Flavobacterium/genética , Fusobactérias/genética , Microbiota/genética , RNA Ribossômico 16S/genética , Rios/microbiologia , Biologia Computacional/métodos , Monitoramento Ambiental/métodos , Peru , Esgotos/microbiologia , Água/análise , Microbiologia da Água , Poluição da Água/análise
18.
BMC Microbiol ; 21(1): 116, 2021 04 17.
Artigo em Inglês | MEDLINE | ID: mdl-33865329

RESUMO

BACKGROUND: To tackle the problem of antibiotic resistance, an extensive search for novel antibiotics is one of the top research priorities. Around 60% of the antibiotics used today were obtained from the genus Streptomyces. The river sediments of Bangladesh are still an unexplored source for antibiotic-producing bacteria (APB). This study aimed to isolate novel APB from Padma and Kapotakkho river sediments having the potential to produce antibacterial compounds with known scaffolds by manipulating their self-protection mechanisms. RESULTS: The antibiotic supplemented starch-casein-nitrate agar (SCNA) media were used to isolate antibiotic-resistant APB from the river sediments. The colonies having Streptomyces-like morphology were selectively purified and their antagonistic activity was screened against a range of test bacteria using the cross-streaking method. A notable decrease of the colony-forming units (CFUs) in the antibiotic supplemented SCNA plates compared to control plates (where added antibiotics were absent) was observed. A total of three azithromycin resistant (AZR) and nine meropenem resistant (MPR) isolates were purified and their antagonistic activity was investigated against a series of test bacteria including Shigella brodie, Escherichia coli, Pseudomonas sp., Proteus sp., Staphylococcus aureus, and Bacillus cereus. All the AZR isolates and all but two MPR isolates exhibited moderate to high broad-spectrum activity. Among the isolates, 16S rDNA sequencing of NAr5 and NAr6 were performed to identify them up to species level. The analyses of the sequences revealed that both belong to the genus Streptomyces. CONCLUSIONS: The results from these studies suggest that manipulation of the self-resistance property of APB is an easy and quick method to search for novel APB having the potential to produce potentially novel antibacterial compounds with known scaffolds.


Assuntos
Antibacterianos/metabolismo , Fenômenos Fisiológicos Bacterianos , Resistência Microbiana a Medicamentos , Sedimentos Geológicos/microbiologia , Interações Microbianas/fisiologia , Streptomyces/fisiologia , Antibacterianos/farmacologia , Bangladesh , RNA Ribossômico 16S/genética , Rios/microbiologia , Streptomyces/efeitos dos fármacos , Streptomyces/genética , Streptomyces/isolamento & purificação
19.
Sci Total Environ ; 778: 146131, 2021 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-33721645

RESUMO

Human activities in rural areas, such as livestock farming, aquaculture, and rural domestic sewage discharge, may result in antibiotic resistance genes (ARGs) pollution in rural rivers. A systematic monitoring in different seasons was conducted in a typical agriculture-polluted river with Real-Time Quantitative PCR. A total of 11 ARGs and 2 related mobile genetic elements (MGEs) were detected at all sites with relative abundances of 6.9 × 10-10-0.2 copies/16S rRNA copies. Among them, sul1, sul2 and int1 were the dominant target genes in water samples. tetW, ermB, and floR were more abundant in November (the dry season), while other ARGs, MGEs and 16s rRNA were at a higher absolute abundance in warm seasons. There was less spatial variation of ARGs in the dry season than in the other two seasons. Furthermore, the relative abundance of ARGs was higher at sampling sites adjoining pollution sources. In addition, cluster analysis implied that ARGs in upstream sediments may be released into surface water and migrate downstream in the direction of river flow. There was no significant correlation between ARGs and their corresponding antibiotics. However, the total concentration of tetracycline was significantly correlated with the non-paired ARGs, including sul3, floR, and ermB. At the same time, heavy metals (Zn, Pb, Cd, Cr6+, As) and other environmental parameters (permanganate index, pH, DO) may apply selective pressure on the spread of ARGs, according to redundancy and Pearson's correlation analysis.


Assuntos
Antibacterianos , Genes Bacterianos , Sequências Repetitivas Dispersas , Rios/microbiologia , Estações do Ano , Antibacterianos/farmacologia , China , Resistência Microbiana a Medicamentos/genética , RNA Ribossômico 16S/genética
20.
PLoS One ; 16(3): e0247910, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33661997

RESUMO

Fundamental ecological principles of ecosystem-level respiration are extensively applied in greenhouse gas and elemental cycle studies. A laboratory system termed CEMS (Carbon Dioxide Evolution Measurement System), developed to explore microbial biofilm growth and metabolic responses, was evaluated as an early-warning system for microbial disturbances in industrial settings: in (a) potable water system contamination, and (b) bioreactor inhibition. Respiration was detected as CO2 production, rather than O2 consumption, including aerobic and anaerobic metabolism. Design, thresholds, and benefits of the remote CO2 monitoring technology were described. Headspace CO2 correlated with contamination levels, as well as chemical (R2 > 0.83-0.96) and microbiological water quality indicators (R2 > 0.78-0.88). Detection thresholds were limiting factors in monitoring drinking water to national and international standards (0 CFU/100 mL fecal coliforms) in both open- (>1500 CFU/mL) and closed-loop CO2 measuring regimes (>100 CFU/100 mL). However, closed-loop detection thresholds allow for the detection of significant contamination events, and monitoring less stringent systems such as irrigation water (<100 CFU/mL). Whole-system respiration was effectively harnessed as an early-warning system in bioreactor performance monitoring. Models were used to deconvolute biological CO2 fluctuations from chemical CO2 dynamics, to optimize this real-time, sustainable, low-waste technology, facilitating timeous responses to biological disturbances in bioreactors.


Assuntos
Dióxido de Carbono/análise , Microbiologia da Água , Anaerobiose , Bactérias/isolamento & purificação , Bactérias/metabolismo , Biofilmes , Reatores Biológicos , Água Potável/microbiologia , Ecossistema , Monitoramento Ambiental , Rios/microbiologia , Águas Residuárias/microbiologia
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