New Insights into the Ecology and Physiology of Methanomassiliicoccales from Terrestrial and Aquatic Environments

Members of the archaeal order Methanomassiliicoccales are methanogens mainly associated with animal digestive tracts. However, environmental members remain poorly characterized as no representatives not associated with a host have been cultivated so far. In this study, metabarcoding screening combined with quantitative PCR analyses on a collection of diverse non-host-associated environmental samples revealed that Methanomassiliicoccales were very scarce in most terrestrial and aquatic ecosystems. Relative abundance of Methanomassiliicoccales and substrates/products of methanogenesis were monitored during incubation of environmental slurries. A sediment slurry enriched in Methanomassiliicoccales was obtained from a freshwater sample. It allowed the reconstruction of a high-quality metagenome-assembled genome (MAG) corresponding to a new candidate species, for which we propose the name of Candidatus ‘Methanomassiliicoccus armoricus MXMAG1’. Comparison of the annotated genome of MXMAG1 with the published genomes and MAGs from Methanomassiliicoccales belonging to the 2 known clades (‘free-living’/non-host-associated environmental clade and ‘host-associated’/digestive clade) allowed us to explore the putative physiological traits of Candidatus ‘M. armoricus MXMAG1’. As expected, Ca. ‘Methanomassiliicoccus armoricus MXMAG1’ had the genetic potential to produce methane by reduction of methyl compounds and dihydrogen oxidation. This MAG encodes for several putative physiological and stress response adaptations, including biosynthesis of trehalose (osmotic and temperature regulations), agmatine production (pH regulation), and arsenic detoxication, by reduction and excretion of arsenite, a mechanism that was only present in the ‘free-living’ clade. An analysis of co-occurrence networks carried out on environmental samples and slurries also showed that Methanomassiliicoccales detected in terrestrial and aquatic ecosystems were strongly associated with acetate and dihydrogen producing bacteria commonly found in digestive habitats and which have been reported to form syntrophic relationships with methanogens.

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Simultaneous Quantification of Vibrio metoecus and Vibrio cholerae with Its O1 Serogroup and Toxigenic Subpopulations in Environmental Reservoirs

Pathogens ◽

10.3390/pathogens9121053 ◽

2020 ◽

Vol 9 (12) ◽

pp. 1053

Author(s):

Tania Nasreen ◽

Nora A. S. Hussain ◽

Mohammad Tarequl Islam ◽

Fabini D. Orata ◽

Paul C. Kirchberger ◽

...

Keyword(s):

Population Dynamics ◽

Vibrio Cholerae ◽

Relative Abundance ◽

Environmental Samples ◽

Opportunistic Pathogen ◽

Inland Waters ◽

Aquatic Environments ◽

Free Living ◽

Simultaneous Quantification ◽

Culture Independent

Vibrio metoecus is a recently described aquatic bacterium and opportunistic pathogen, closely related to and often coexisting with Vibrio cholerae. To study the relative abundance and population dynamics of both species in aquatic environments of cholera-endemic and cholera-free regions, we developed a multiplex qPCR assay allowing simultaneous quantification of total V. metoecus and V. cholerae (including toxigenic and O1 serogroup) cells. The presence of V. metoecus was restricted to samples from regions that are not endemic for cholera, where it was found at 20% of the abundance of V. cholerae. In this environment, non-toxigenic O1 serogroup V. cholerae represents almost one-fifth of the total V. cholerae population. In contrast, toxigenic O1 serogroup V. cholerae was also present in low abundance on the coast of cholera-endemic regions, but sustained in relatively high proportions throughout the year in inland waters. The majority of cells from both Vibrio species were recovered from particles rather than free-living, indicating a potential preference for attached versus planktonic lifestyles. This research further elucidates the population dynamics underpinning V. cholerae and its closest relative in cholera-endemic and non-endemic regions through culture-independent quantification from environmental samples.

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First report on phytoplankton communities of Barishal City, Bangladesh

Current Botany ◽

10.25081/cb.2020.v11.6296 ◽

2020 ◽

pp. 142-147

Author(s):

Shaswati Chakraborty ◽

Dipalok Karmaker ◽

Subroto Kumar Das ◽

Riyad Hossen

Keyword(s):

Aquatic Ecosystems ◽

Species Number ◽

Aquatic Environments ◽

Primary Producers ◽

First Report ◽

Biodiversity Indices ◽

Phytoplankton Communities ◽

Living Organisms ◽

The City ◽

Total Species

Phytoplanktons, also called microalgae, are microscopic photosynthetic living organisms that generally found in aquatic environments. Although they are considered as the most important primary producers and bioindicators of aquatic ecosystems, there was no previous report found for Barishal City about these tiny organisms. Consequently, the present study selected 10 freshwater reservoirs from the city to investigate phytoplankton communities and listed 110 taxa under 4 phyla, 7 classes, 18 orders, 24 families and 49 genera. The distribution of Chlorophytes was abundant relatively in terms of species number (45 taxa) followed by Euglenophytes, Chlorophytes and Cyanophytes in this area. Only Euglenaceae possessed one-third of the total species of this report. Among all stations, the highest number of taxa was recorded from station 2 and according to nine biodiversity indices, the station 2 and 9 showed comparatively good results. All of the recorded taxa were previously mentioned by different authors from Bangladesh.

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Mitigation of Expression of Virulence Genes in Legionella pneumophila Internalized in the Free-Living Amoeba Willaertia magna C2c Maky

Pathogens ◽

10.3390/pathogens9060447 ◽

2020 ◽

Vol 9 (6) ◽

pp. 447 ◽

Cited By ~ 1

Author(s):

Rayane Mouh Mameri ◽

Jacques Bodennec ◽

Laurent Bezin ◽

Sandrine Demanèche

Keyword(s):

Gene Expression ◽

Legionella Pneumophila ◽

Virulence Genes ◽

Natural Habitat ◽

Acanthamoeba Castellanii ◽

Severe Form ◽

Aquatic Environments ◽

Free Living ◽

Intracellular Parasites ◽

Free Living Amoeba

Legionella pneumophila is a human pathogen responsible for a severe form of pneumonia named Legionnaire disease. Its natural habitat is aquatic environments, being in a free state or intracellular parasites of free-living amoebae, such as Acanthamoeba castellanii. This pathogen is able to replicate within some amoebae. Willaertia magna C2c Maky, a non-pathogenic amoeba, was previously demonstrated to resist to L. pneumophila and even to be able to eliminate the L. pneumophila strains Philadelphia, Lens, and Paris. Here, we studied the induction of seven virulence genes of three L. pneumophila strains (Paris, Philadelphia, and Lens) within W. magna C2c Maky in comparison within A. castellanii and with the gene expression level of L. pneumophila strains alone used as controls. We defined a gene expression-based virulence index to compare easily and without bias the transcript levels in different conditions and demonstrated that W. magna C2c Maky did not increase the virulence of L. pneumophila strains in contrast to A. castellanii. These results confirmed the non-permissiveness of W. magna C2c Maky toward L. pneumophila strains.

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The need to account for cell biology in characterizing predatory mixotrophs in aquatic environments

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2019.0090 ◽

2019 ◽

Vol 374 (1786) ◽

pp. 20190090 ◽

Cited By ~ 7

Author(s):

Susanne Wilken ◽

Charmaine C. M. Yung ◽

Maria Hamilton ◽

Kenneth Hoadley ◽

Juliana Nzongo ◽

...

Keyword(s):

Organic Matter ◽

Single Cell ◽

Gold Standard ◽

Cell Biology ◽

Aquatic Ecosystems ◽

Eukaryotic Cells ◽

Food Chains ◽

Aquatic Environments ◽

Unicellular Eukaryotes ◽

Aquatic Food

Photosynthesis in eukaryotes first arose through phagocytotic processes wherein an engulfed cyanobacterium was not digested, but instead became a permanent organelle. Other photosynthetic lineages then arose when eukaryotic cells engulfed other already photosynthetic eukaryotic cells. Some of the resulting lineages subsequently lost their ability for phagocytosis, while many others maintained the ability to do both processes. These mixotrophic taxa have more complicated ecological roles, in that they are both primary producers and consumers that can shift more towards producing the organic matter that forms the base of aquatic food chains, or towards respiring and releasing CO 2 . We still have much to learn about which taxa are predatory mixotrophs as well as about the physiological consequences of this lifestyle, in part, because much of the diversity of unicellular eukaryotes in aquatic ecosystems remains uncultured. Here, we discuss existing methods for studying predatory mixotrophs, their individual biases, and how single-cell approaches can enhance knowledge of these important taxa. The question remains what the gold standard should be for assigning a mixotrophic status to ill-characterized or uncultured taxa—a status that dictates how organisms are incorporated into carbon cycle models and how their ecosystem roles may shift in future lakes and oceans. This article is part of a discussion meeting issue ‘Single cell ecology’.

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The human pathogenic vibrios – A public health update with environmental perspectives

Epidemiology and Infection ◽

10.1017/s0950268800030326 ◽

1989 ◽

Vol 103 (1) ◽

pp. 1-34 ◽

Cited By ~ 61

Author(s):

P. A. West

Keyword(s):

Public Health ◽

Acute Infection ◽

Aquatic Environments ◽

Free Living ◽

Liver Disorders ◽

Naturally Occurring ◽

Pathogenic Vibrio ◽

Ear Infections ◽

Pathogenic Vibrios ◽

Living Bacteria

PathogenicVibriospecies are naturally-occurring bacteria in freshwater and saline aquatic environments. Counts of free-living bacteria in water are generally less than required to induce disease. Increases in number of organisms towards an infective dose can occur as water temperatures rise seasonally followed by growth and concentration of bacteria on higher animals, such as chitinous plankton, or accumulation by shellfish and seafood. PathogenicVibriospecies must elaborate a series of virulence factors to elicit disease in humans.Activities which predispose diarrhoeal and extraintestinal infections include ingestion of seafood and shellfish and occupational or recreational exposure to natural aquatic environments, especially those above 20 °C. Travel to areas endemic for diseases due to pathogenicVibriospecies may be associated with infections. Host risk factors strongly associated with infections are lack of gastric acid and liver disorders.Involvement of pathogenicVibriospecies in cases of diarrhoea should be suspected especially if infection is associated with ingestion of seafood or shellfish, raw or undercooked, in the previous 72 h.Vibriospecies should be suspected in any acute infection associated with wounds sustained or exposed in the marine or estuarine environment. Laboratories serving coastal areas where infection due to pathogenic Vibrio species are most likely to occur should consider routine use of TCBS agar and other detection regimens for culture ofVibriospecies from faeces, blood and samples from wound and ear infections.

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Bacterial growth response to copepod grazing in aquatic ecosystems

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315407056275 ◽

2007 ◽

Vol 87 (3) ◽

pp. 667-674 ◽

Cited By ~ 8

Author(s):

Cristian A. Vargas ◽

L. Antonio Cuevas ◽

Humberto E. González ◽

Giovanni Daneri

Keyword(s):

Food Web ◽

Bacterial Growth ◽

Bacterial Communities ◽

Aquatic Ecosystems ◽

Field Measurements ◽

Zooplankton Biomass ◽

Aquatic Environments ◽

Coastal Embayment ◽

Copepod Grazing ◽

Bacterial Assemblages

The growth rate response of bacterial communities to the potential increase of dissolved organic matter (DOM) produced by the copepod Acartia tonsa was assessed in experiments conducted in three stations representing three contrasting aquatic environments (coastal embayment, shelf and ocean). Bacterial assemblages were inoculated in filtered seawater where A. tonsa had previously grazed. Utilization of DOM over time was evaluated after the addition of bacterial inoculums as the biomass changes in both ‘control’ and ‘copepod’ treatments. In the embayment and ocean a high bacterial growth was observed in the treatments with seawater where copepod were feeding. Additional field measurements of bacterial, primary production and zooplankton biomass support the idea that bacterial communities living in oceanic environments can be efficient to utilize the newly available substrate. Copepods play a key role not only as conveyors of carbon up through the classical food-web, but also generated significant amounts of bacterial substrate in the microbial loop food-web.

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Environmental Fate of Polychlorinated Dibenzo-p-dioxins in Lake Enclosures

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/f92-081 ◽

1992 ◽

Vol 49 (4) ◽

pp. 722-734 ◽

Cited By ~ 13

Author(s):

Mark R. Servos ◽

Derek C. G. Muir ◽

G. R. Barrie Webster

Keyword(s):

Organic Matter ◽

Water Column ◽

Particulate Organic Matter ◽

Environmental Fate ◽

Aquatic Environments ◽

Surficial Sediments ◽

Experimental Lakes Area ◽

Northwestern Ontario ◽

Chlorine Substitution ◽

Sediment Slurry

The environmental fate of 1,3,6,8-tetra- (T4CDD) and octachlorodibenzo-p-dioxin (O8CDD), two major dioxin congeners emitted into the environment, was studied in large (40 m3) lake enclosures at the Experimental Lakes Area in northwestern Ontario. The polychlorinated dioxins (PCDDs) were added to replicate enclosures as a sediment slurry at a nominal concentration of 58–59 ng∙L−1. Both congeners partitioned/settled rapidly to the surficial sediments where they persisted over the 2 yr of the study. Initially the concentrations of the T4CDD in water were higher than those of O8CDD, but the concentrations of the T4CDD in the water column declined more rapidly than those of O8CDD, with t1/2 of 2.6 ± 0.2 and 4.0 ± 0.3 d, respectively. Approximately 10–15% of the T4CDD and < 1% of the O8CDD detected in the water column during the first 48 h were determined to be truly dissolved. The rapid partitioning of O8CDD and to a lesser extent T4CDD to dissolved and particulate organic matter in the water column and sediments limited their bioavailability. Increased retentive capacity of the higher chlorinated PCDDs may explain the pattern of increasing concentration of PCDDs in sediments with increasing chlorine substitution observed in the Great Lakes and other aquatic environments.

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Optimisation of an extraction/leaching procedure for the characterisation and quantification of titanium dioxide (TiO2) nanoparticles in aquatic environments using SdFFF-ICP-MS and SEM-EDX analyses

Analytical Methods ◽

10.1039/c7ay00635g ◽

2017 ◽

Vol 9 (24) ◽

pp. 3626-3635 ◽

Cited By ~ 6

Author(s):

Florian Dutschke ◽

Johanna Irrgeher ◽

Daniel Pröfrock

Keyword(s):

Titanium Dioxide ◽

Tio2 Nanoparticles ◽

Environmental Samples ◽

Extraction Method ◽

Nano Particles ◽

Aquatic Environments ◽

Ms Analysis ◽

Icp Ms ◽

Edx Analyses ◽

Leaching Procedure

A novel, optimized and validated extraction method for engineered TiO2 nano-particles from environmental samples prior to SdFFF-MALS-ICP-MS/MS analysis is presented.

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Diversity of Antimicrobial-Resistant Aeromonas Species Isolated from Aquatic Environments in Brazil

10.1101/2020.06.23.168385 ◽

2020 ◽

Author(s):

Danieli Conte ◽

Jussara Kasuko Palmeiro ◽

Adriane de Almeida Bavaroski ◽

Luiza Souza Rodrigues ◽

Daiane Cardozo ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Resistance Genes ◽

Aquatic Ecosystems ◽

Bacterial Resistance ◽

Genetic Relatedness ◽

Anthropogenic Activities ◽

Treatment Plant ◽

Aeromonas Species ◽

Aquatic Environments ◽

Antimicrobial Resistance Genes

ABSTRACTIn the present study, we characterized antimicrobial resistance profile and genetic relatedness of Aeromonas spp. isolated from healthcare and urban effluents, wastewater treatment plant (WWTP), and river water. We detected the presence of genes responsible for the resistance to β-lactam, quinolone, and aminoglycoside. Enterobacterial Repetitive Intergenic Consensus PCR and multilocus sequence typing (MLST) were carried out to differentiate the strains and multilocus phylogenetic analysis (MLPA) was used to identify species. A total of 28 Aeromonas spp. cefotaxime-resistant strains were identified that carried a variety of resistance determinants, including uncommon GES-type β-lactamases. Multidrug-resistant Aeromonas spp. were found in hospital wastewater, WWTP, and sanitary effluent. Among these isolates, we detected A. caviae producing GES-1 or GES-5, as well as A. veronii harboring GES-7 or GES-16. We successfully identified Aeromonas spp. by using MLPA and found that A. caviae was the most prevalent species (85.7%). In contrast, it was not possible to determine sequence type of all isolates, suggesting incompleteness of the Aeromonas spp. MLST database. Our findings reinforce the notion about the ability of Aeromonas spp. to acquire determinants of antimicrobial resistance from the environment. Such ability can be enhanced by the release of untreated healthcare effluents, in addition to the presence of antimicrobials, recognized as potential factors for the spread of resistance. Thus, Aeromonas spp. could be included as priority pathogens under the One Health concept.IMPORTANCEAeromonas species are native bacteria in aquatic ecosystems worldwide. However, they have also been isolated from humans and animals. Globally, aquatic environments have been affected by anthropogenic activities. For example, the excessive use of antimicrobials in medical and veterinary practice causes the development of bacterial resistance. In addition, eliminated hospital and sanitary effluents can also serve as potential sources of bacteria carrying antimicrobial resistance genes. Thereby, impacted environments play an important role in the transmission of these pathogens, their evolution, and dissemination of genes conferring resistance to antimicrobials. Aeromonas spp. have been reported as a reservoir of antimicrobial resistance genes in the environment. In this study, we identified a great repertoire of antimicrobial resistance genes in Aeromonas spp. from diverse aquatic ecosystems, including those that encode enzymes degrading broad-spectrum antimicrobials widely used to treat healthcare-associated infections. These are a public health threat as they may spread in the population.

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Ecological Divergence Within the Enterobacterial Genus Sodalis: From Insect Symbionts to Inhabitants of Decomposing Deadwood

Frontiers in Microbiology ◽

10.3389/fmicb.2021.668644 ◽

2021 ◽

Vol 12 ◽

Author(s):

Vojtěch Tláskal ◽

Victor Satler Pylro ◽

Lucia Žifčáková ◽

Petr Baldrian

Keyword(s):

Carbon Sources ◽

Tsetse Fly ◽

Rrna Gene ◽

Ecological Divergence ◽

Free Living ◽

Multiple Loci ◽

Genetic Potential ◽

Nitrogenase Genes ◽

Living Species ◽

Insect Symbionts

The bacterial genus Sodalis is represented by insect endosymbionts as well as free-living species. While the former have been studied frequently, the distribution of the latter is not yet clear. Here, we present a description of a free-living strain, Sodalis ligni sp. nov., originating from decomposing deadwood. The favored occurrence of S. ligni in deadwood is confirmed by both 16S rRNA gene distribution and metagenome data. Pangenome analysis of available Sodalis genomes shows at least three groups within the Sodalis genus: deadwood-associated strains, tsetse fly endosymbionts and endosymbionts of other insects. This differentiation is consistent in terms of the gene frequency level, genome similarity and carbohydrate-active enzyme composition of the genomes. Deadwood-associated strains contain genes for active decomposition of biopolymers of plant and fungal origin and can utilize more diverse carbon sources than their symbiotic relatives. Deadwood-associated strains, but not other Sodalis strains, have the genetic potential to fix N2, and the corresponding genes are expressed in deadwood. Nitrogenase genes are located within the genomes of Sodalis, including S. ligni, at multiple loci represented by more gene variants. We show decomposing wood to be a previously undescribed habitat of the genus Sodalis that appears to show striking ecological divergence.

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