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The present study assessed the abiotic factors of Moringa stenopetala (M. stenopetala) extracts against Staphyloccoccus aureus in aquatic microcosm. Bacterial survival was assessed using colony forming unit (CFU) method on culture agar medium at different concentration levels (0.5 to 2 g/L). The incubation duration varied from 3 to 24 hours, and the temperatures were between 7°C and 44°C. Phytochemical screening showed that most of the constituents obtained from the extracts are the alkaloids, flavonoids and the tannins. It was observed that increase in extract concentration significantly inhibited the number of CFU obtained. Compared to the control {9.27 Log(CFU/100 mL)}, cells abundance from different concentrations of leaves extracts fluctuated between 4.74 and 0 {Log(CFU/100 mL)} after 3h incubation; 5.46 and 0 {Log(CFU/100 mL)} after 6h; 4.75 and 0 {Log(CFU̸/100 mL)} after 9h, and 4.85 and 0 {Log(CFU/100 mL)} after 24h incubation. As for root extracts, the abundance were between 4.80 and 0 {Log(CFU/100 mL)} under 7°C incubation; 5.03-5.23 and 0 {Log(CFU/100 mL)} under 23°C and 37°C, and 4.66 and 0 Log (CFU/100 mL) under 44°C incubation when considering the whole extract concentrations used. Incubation temperature and extracts concentration significantly impacted bacterial abundances. When the decoction extracts of roots were used, the amount of S. aureus cells inhibited was registered after 3-24 hours incubation. The Pearson correlation coefficient in most cases, revealed an inversely proportional relationship between the plant extracts and S. aureus cultured cells in a dose-dependent manner (P≤0.05). The use of M. stenopetala extracts could constitute an alternative in the treatment of water intended for human consumption.

A study was carried out on Aeromonashydrophilaadhesion to polythene fragment at different cell growth phases in aquatic microcosm. The main purpose of this study was to assess adsorption capacity, adsorption intensity and kinetics of Aeromonashydrophilaon polythene in sodium hypochlorite(NaOCl) andhydrogen peroxide (H2O2)disinfected water.The mean abundance of adheredA. hydrophilasometimes reached 28 and 111CFU.cm-2respectively in NaOCl and H2O2treated water. The adsorption capacities of A. hydrophilacells fluctuated between 1 and 2.12x1057and between 1 and 2.29x1027adhered cells.cm-2in NaOCl and H2O2disinfected water respectively. The adsorption intensities of this bacterium ranged from -45.81 to 3.49x1019and from 0.16 to 2.29x1027respectively in NaOCl and H2O2treated water. Adsorption capacity and adsorption intensity of A. hydrophilacells on polythene in NaOCl treated water were greater than that obtained in water disinfected with H2O2. Adhesion kinetics of A. hydrophilacells oscillated between 0.001 and 0.930 adhered cell.cm-2.h-1. Adsorption kinetics seem resulted from interactions between bacterial cells and substrates, and depended both on the fragment type and bacterial species. The values of A. hydrophilasurface hydrophobicity fluctuated between 65.11 and 92.74% in NaOCl disinfected water and between 63.38 and 89.41% in H2O2 treated water. The mean values of contact angle ranged from 83.1±0.6 to 85.8±0.8°.Adhesion of A. hydrophilaon polythene is mediated amongst others by cell growth phases, cell surface hydrophobicity, cell kinetic adhesion, adsorption capacity and adsorption intensity.

Increasing human activity has raised concerns about the impact of deposition of anthropogenic combustion aerosols (i.e., black carbon; BC) on marine processes. The sea surface microlayer (SML) is a key gate for the introduction of atmospheric BC into the ocean; however, relatively little is known of the effects of BC on bacteria-virus interactions, which can strongly influence microbially mediated processes. To study the impact of BC on bacteria-virus interactions, field investigations involving collection from the SML and underlying water were carried out in Halong Bay (Vietnam). Most inorganic nutrient concentrations, as well as dissolved organic carbon, were modestly but significantly higher ('p' = 0.02–0.05) in the SML than in underlying water. The concentrations of particulate organic carbon (though not chlorophyll 'a') and of total particulate carbon, which was composed largely of particulate BC (mean = 1.7 ± 6.4 mmol L–1), were highly enriched in the SML, and showed high variability among stations. On average, microbial abundances (both bacteria and viruses) and bacterial production were 2- and 5fold higher, respectively, in the SML than in underlying water. Significantly lower bacterial production ('p' < 0.01) was observed in the particulate fraction (>3 μm) compared to the bulk sample, but our data overall suggest that bacterial production in the SML was stimulated by particulate BC. Higher bacterial production in the SML than in underlying water supported high viral lytic infection rates (from 5.3 to 30.1%) which predominated over percent lysogeny (from undetected to 1.4%). The sorption of dissolved organic carbon by black carbon, accompanied by the high lytic infection rate in the black carbon-enriched SML, may modify microbially mediated processes and shift the net ecosystem metabolism (ratio of production and respiration) to net heterotrophy and CO2 production in this critical layer between ocean and atmosphere.

Microbial food web dynamics were determined during the onset of several spring phytoplankton blooms induced by natural iron fertilization off Kerguelen Island in the Southern Ocean (KEOPS2). The abundances of heterotrophic bacteria and heterotrophic nanoflagellates, bacterial heterotrophic production, bacterial respiration, and bacterial growth efficiency, were consistently higher in surface waters of the iron-fertilized sites than at the reference site in HNLC (high nutrient low chlorophyll) waters. The abundance of virus-like particles remained unchanged, but viral production increased by a factor of 6 in iron-fertilized waters. Bacterial heterotrophic production was significantly related to heterotrophic nanoflagellate abundance and viral production across all sites, with bacterial production explaining about 70 and 85%, respectively, of the variance of each in the mixed layer (ML). Estimated rates of grazing and viral lysis, however, indicated that heterotrophic nanoflagellates accounted for a substantially higher loss of bacterial production (50%) than viruses (11%). Combining these results with rates of primary production and export determined for the study area, a budget for the flow of carbon through the microbial food web and higher trophic levels during the early (KEOPS2) and the late phase (KEOPS1) of the Kerguelen bloom is provided.

The abundance and activity of the major members of the heterotrophic microbial community – from viruses to ciliates – were studied along a longitudinal transect across the Mediterranean Sea in the summer of 2008. The Mediterranean Sea is characterized by a west to-east gradient of deepening of DCM (deep chlorophyll maximum) and increasing oligotrophy reflected in gradients of biomass and production. However, within this well documented longitudinal trend, hydrological mesoscale features exist and likely influence microbial dynamics. Here we present data from a W-E transect of 17 stations during the period of summer stratification. Along the transect the production and fate of organic matter was investigated at three selected sites each one located in the centre of an anticyclonic eddy: in the Algero-Provencal Basin (St. A), the Ionian Basin (St. B), and the Levantine Basin (St. C). The 3 geographically distant eddies showed low values of the different heterotrophic compartments of the microbial food web, and except for viruses in site C, all integrated (0–150 m) stocks were higher in reference stations located in the same basin outside the eddies. During our study the 3 eddies showed equilibrium between GPP (Gross Primary Production) and DCR (Dark Community Respiration). Integrated PPp (Particulate Primary Production) values at A, B and C varied from ~140 to ~190 mg C m−2.

Fluctuations in total nitrogen and phosphorus concentrations and in the N/P ratio (i.e. in terms of mass) were measured at the entry and exit of the Sahela Reservoir (Morocco) throughout an annual cycle. Particulate N and P concentrations in sedimenting particles in the reservoir itself were also measured. The results obtained showed that the spring floods were a major source of N and P inputs, this being especially pronounced for phosphorus that was present mainly in particulate form. In all the compartments of the reservoir analysed, the N/P ratios were high (means between 81 and 314), especially in summer (the only season when the reservoir was emptied) when the supply of P was apparently limited by the drought. However, the values of this ratio in the sedimenting particles remained lower (mean = 21), at levels characteristic of natural communities. This implies that the reservoir's biological communities preferentially store phosphorus, no doubt to maximise their activity in an environment where a large proportion of this element is not bioavailable. Furthermore, it appeared that the quantity of particulate N and P sequestrated by the sediments and the total quantities of N and P leaving the reservoir were greater than the inputs of these nutrients, underlining the importance of lateral and internal nutrient supplies. One spot measurement, made in a single month, showed that nutrient release activity from the sediments was in fact quite considerable. [ABSTRACT FROM AUTHOR]

To investigate the deteriorating bacteriological water quality of Municipal Lake of Yaoundé, the degree of pollution of the Mingoa Stream, the main tributary of the lake, was evaluated for total coliforms, thermotolerant coliforms, and fecal streptococci. Concentrations of these bacterial indicators in Mingoa Stream were higher than those allowed by international norms for the bacteriological quality of recreational water. Thus, this stream contributes to the high levels of bacteria number in the water column of the Municipal Lake. [ABSTRACT FROM AUTHOR]

The coastal waters of Kerala, in the South Eastern Arabian Sea (SEAS), are unique during the Southwest monsoon season due to the concurrent occurrence of two physical processes, the upwelling and Mudbanks. However, little is known about the viral ecology and activity in a system where upwelling and Mudbanks coexist, though it is generally recognized that microbial assemblages play a vital role in the food web dynamics of marine systems, particularly in upwelling. Water samples were taken from monsoon and pre-monsoon period from three locations, (M1, M2, and M3) off Alappuzha, on the southwest coast of India to examine the viral activity and distribution. The dissolved oxygen levels showed the incursion of hypoxic waters in all the stations during the peak upwelling period. Upwelling signals were prominent in all the stations, but Mudbank and upwelling co-occurred at M2 alone during monsoon. The abundance of viruses ranged from 0.86 to 15.68 × 10 6 Viral-like Particles (VLPs mL -1 ) and prokaryotic abundance ranged from 2.73-16.26 × 10 5 cells mL -1 . Viral and prokaryotic abundance was significantly higher in the monsoon compared to pre and late-monsoon. Based on Transmission electron microscopy (TEM) results, the non-tailed viruses constituted the major (43%) proportion of the total viruses in this study region. However, the viral production rates and viral-mediated bacterial mortality were high in the pre-monsoon compared to the monsoon and late-monsoon periods. There was no obvious effect of Mudbanks on viral dynamics and the observed variations in virological and hydrological features were governed mainly by coastal upwelling., (© 2024. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

The smallest entities in aquatic ecosystems, i.e., femtoplankton, are certainly the largest reservoir of uncharacterized biodiversity. Among them, the discovery of mysterious Aster like nanoparticles has raised many questions about their nature, origin and ecology. Here, we highlight the original nature of this new model, organic and composed of enriched-calcium carbohydrates, with no detection of nucleic acids or proteins. The biosynthesis of these entities seems to be associated with a host in their 11 arms' form prior to their release into the environment. An intriguing aspect of their mode of development is their ability, once free, to change form and maintain their abundance autonomously without metabolism being detected, resulting in an unexpected polymorphism. Their remarkable capacity for massive in situ development and their links with prokaryotes and other microbes suggest a major role in the functioning of aquatic ecosystems. There's no doubt that these new entities are a source of new knowledge not only in the sciences of organic nanoparticles, but also in their ecological importance for aquatic ecosystems., (© 2024. The Author(s).)

Kribi is a seaside town that welcomes thousands of tourists each year. However, the poor sanitation condition of its beaches along the Atlantic coast is not without risk for visitors. In this study, we used the formol-ether concentration technique to identify and quantify larvae or eggs of intestinal helminths in waters of three regularly visited Kribi beaches (Mpalla, Ngoyè, and Mboamanga). Results revealed that all identified larvae and eggs were cestodes ( Hymenolepis nana ) and nematodes ( Strongyloides sp., Ascaris sp., Ancylostoma duodenale and Trichuris trichiura ). All the helminth eggs and larvae showed high abundance at low tide during rainy seasons. Ancylostoma duodenale eggs, totally absent at Mpalla, were densely present at low tide at Ngoyè (301 ± 15 eggs/L). Trichuris trichiura eggs showed the lowest abundance (0 to 62 eggs/L) at all sites. Abiotic variables indicated that waters at the various beaches were basic (pH: 8.75-9.77), generally warmer (32.44°C at Mpalla in the Short Rainy Season), more oxygenated at low tide, and moderately mineralized at high tide. Positive and significant correlations were observed at Ngoyè at low tide between Strongyloides sp. larvae and dissolved oxygen ( P ˂ 0.05); and between Ancylostoma duodenale eggs and temperature ( P ˂ 0.05). The overall results indicated that the beaches studied are subjected to fecal pollution. This pollution is more accentuated during low tides than during high tides. Depending on tidal movements, swimmers risk exposure to helminth eggs and larvae known to be responsible for gastroenteritis.

The development of new technologies of microscopy, flow cytometry and genomics has allowed a profound reconsideration of the diversity and ecological role of femtoplankton entities (i.e., viruses, vesicles, aster like nanoparticles -ALNs-). Among these, the discovery of ALNs, raise serious questions about their exact nature and their biological and environmental roles. The elaboration of a practical guide for the concentration and separation of femtoplankton entities, including ALNs, is necessary for a better understanding of their diversity, ontogeny, and ecology. Here, we propose a step-by-step procedure for the enrichment and isolation of femtoplankton entities and prokaryotes. The established protocol couples tangential flow filtration to differential centrifugation, leading to differentiate enriched samples (with different target entity contents), usable as a matrix for sorting by flow cytometry. All entities were identified, characterized and counted by transmission electron microscopy and flow cytometry. The procedure allows an efficient detection, concentration and separation of femtoplankton entities (up to purity rate of 92, 67, 81 and 85% for virus like particles, vesicles, prokaryotes and ALNs, respectively), and different morphotypes of ALNs into different fractions (up to 51, 72, 52, 40 and 79% of total ALNs for 20-, 11-, budding 11-, 5-10- and 4-armed ALNs, respectively)., Competing Interests: Declaration of Competing Interest The authors declare no conflict of interest., (Copyright © 2023 Elsevier B.V. All rights reserved.)

In aquatic environments, the consensus of viral impact on bacterial carbon metabolism with the nutrient environment as an important axis is limited. Henceforth, we explored the viral regulation of carbon-based bacterial growth efficiency (BGE) in a set of freshwater systems from French Massif Central, which were broadly classified based on two trophic statuses: eutrophic and non-eutrophic lakes. Comparative analysis showed that microbial abundances (viruses and bacteria) were 3-fold higher in eutrophic compared with non-eutrophic lakes, and so were bacterial production and viral lytic infection. The observed variability in BGE (10-60%) was explained by the uncoupling between bacterial respiration and production. Viruses through selective lysis of susceptible host communities had an antagonistic impact on BGE in the eutrophic lakes, whereas the release of substrates via viral shunt exerted a synergistic influence on the carbon metabolism of non-targeted host populations in non-eutrophic lakes. The decisive effect of the two individual processes (i.e., lysis and substrate release) on BGE was supported by regressions of bacterial abundance as a function of bacterial production, which is considered as a proxy of top-down processes. The role of viruses through their negative impact via mortality and positive impact via substrate supply can eventually have implications on carbon transfer through bacterioplankton in freshwaters.

Aster-like nanoparticles (ALNs) are femtoentities, recently discovered in different aquatic environments, whose intrinsic nature and ecological features remain to be determined. In this study, we investigate the in situ temporal dynamics of ALNs during 1 year in 3 different lakes, in relation to the physico-chemical and biological environment. ALN abundances in investigated lakes showed a marked seasonal dynamic (from no detectable to 4.28 ± 0.75 × 10 6 ALNs mL -1 ), with characteristic peaks in spring. We recorded a correlation between ALNs and some prokaryotic phyla suggesting a broad and non-specific relationship. From their seasonal dynamics and potential link with prokaryotes, we conclude that ALNs represent an important ecological actor in the functioning of aquatic ecosystems., (© 2022. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Small circular single-stranded DNA viruses of the Microviridae family are both prevalent and diverse in all ecosystems. They usually harbor a genome between 4.3 and 6.3 kb, with a microvirus recently isolated from a marine Alphaproteobacteria being the smallest known genome of a DNA phage (4.248 kb). A subfamily, Amoyvirinae , has been proposed to classify this virus and other related small Alphaproteobacteria-infecting phages. Here, we report the discovery, in meta-omics data sets from various aquatic ecosystems, of sixteen complete microvirus genomes significantly smaller (2.991-3.692 kb) than known ones. Phylogenetic analysis reveals that these sixteen genomes represent two related, yet distinct and diverse, novel groups of microviruses- amoyviruses being their closest known relatives. We propose that these small microviruses are members of two tentatively named subfamilies Reekeekeevirinae and Roodoodoovirinae . As known microvirus genomes encode many overlapping and overprinted genes that are not identified by gene prediction software, we developed a new methodology to identify all genes based on protein conservation, amino acid composition, and selection pressure estimations. Surprisingly, only four to five genes could be identified per genome, with the number of overprinted genes lower than that in phiX174. These small genomes thus tend to have both a lower number of genes and a shorter length for each gene, leaving no place for variable gene regions that could harbor overprinted genes. Even more surprisingly, these two Microviridae groups had specific and different gene content, and major differences in their conserved protein sequences, highlighting that these two related groups of small genome microviruses use very different strategies to fulfill their lifecycle with such a small number of genes. The discovery of these genomes and the detailed prediction and annotation of their genome content expand our understanding of ssDNA phages in nature and are further evidence that these viruses have explored a wide range of possibilities during their long evolution., (© The Author(s) 2023. Published by Oxford University Press.)

Fungal parasitism is common in plankton communities and plays a crucial role in the ecosystem by balancing nutrient cycling in the food web. Previous studies of aquatic ecosystems revealed that zoosporic chytrid epidemics represent an important driving factor in phytoplankton seasonal successions. In this study, host-parasite dynamics in Lake Pavin (France) were investigated during the spring diatom bloom while following chytrid epidemics using next generation sequencing (NGS). Metabarcoding analyses were applied to study changes in the eukaryotic microbial community throughout diatom bloom-chytrid epidemics. Relative read abundances of metabarcoding data revealed potential "beneficiaries" and "victims" during the studied period. Subsequently, metatranscriptomic analyses on samples before and during the chytrid epidemic unveiled the active part of the community and functional/metabolic dynamics in association with the progress of chytrid infection. Diatom functions involving lipases, transporters, histones, vacuolar systems, the proteasome, proteases and DNA/RNA polymerases were more abundant during the diatom bloom. Chytrid functions related to a parasitic lifestyle including invasion, colonization and stress tolerance were up-regulated during the chytrid epidemic. In addition, functions related to the degradation/metabolism of proteins, lipids and chitin were in higher proportion in the community during the epidemic event. Results of NGS and bioinformatics analyses offered a panorama of dynamic biodiversity and biological functioning of the community., (© 2022 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)

Hysterocinetida are a large assemblage of ciliates characterized by sucker and buccal apparatus. They have a wide distribution in the digestive tract of oligochaete annelids of the genus Alma that inhabit hydromorphic parts of non-anthropic hydrosystems. On the basis of morphological, morphometric and infraciliature characteristics revealed by ammoniacal silver carbonate and 4',6-Diamidino-2-Phenyl Indole (DAPI) staining techniques, four forms were identified as new members belonging to three genera: Preptychostomum, Proptychostomum and Thurstonia. Preptychostomum donendaensis n. sp. is ovoid with a slightly narrowed anterior part and is commensal to the digestive tract of Alma emini and A. nilotica. There are 20-23 kineties on the lower side and 42-45 on the upper side. Proptychostomum gigas n. sp. is pear-shaped, with a narrowed anterior part and a wide posterior part (125-138 µm × 80-85 µm). There are 40 to 44 kineties, equally distributed on both sides of the ciliate. Its sucker is circular and measures 31-34 µm in diameter. The peristome follows the contour of the cell and the infundibulum has a turn of spire. Thurstonia emini n. sp. is identified in the digestive tract of A. emini. The cell is elongate, with the anterior pole narrower than the truncate posterior pole (90-115 µm × 40-55 µm). The kineties are equally distributed on both sides of the ciliate. The sucker is in the shape of an inverted U. Thurtonia nilotica n. sp. is commensal of the digestive tract of A. nilotica. The cell is pear-shaped, with the anterior part narrowed and the posterior part swollen (110-114 µm × 85-92 µm). 46 to 50 kineties are unevenly distributed on both sides of the ciliate. The sucker is shaped like an inverted lunar crescent.

Microbial communities in lakes can profoundly impact biogeochemical processes through their individual activities and collective interactions. However, the complexity of these communities poses challenges, particularly for studying rare organisms such as Candidate Phyla Radiation bacteria (CPR) and enigmatic entities such as aster-like nanoparticles (ALNs). Here, a reactor was inoculated with water from Lake Fargette, France, and maintained under dark conditions at 4°C for 31 months and enriched for ALNs, diverse Planctomycetes , and CPR bacteria. We reconstructed draft genomes and predicted metabolic traits for 12 diverse Planctomycetes and 9 CPR bacteria, some of which are likely representatives of undescribed families or genera. One CPR genome representing the little-studied lineage " Candidatus Peribacter" was curated to completion (1.239 Mbp) and unexpectedly encodes the full gluconeogenesis pathway. Metatranscriptomic data indicate that some planctomycetes and CPR bacteria were active under the culture conditions, accounting for ∼30% and ∼1% of RNA reads mapping to the genome set, respectively. We also reconstructed genomes and obtained transmission electron microscope images for numerous viruses, including one with a >300-kbp genome and several predicted to infect Planctomycetes . Together, our analyses suggest that freshwater Planctomycetes are central players in a subsystem that includes ALNs, symbiotic CPR bacteria, and viruses. IMPORTANCE Laboratory incubations of natural microbial communities can aid in the study of member organisms and their networks of interaction. This is particularly important for understudied lineages for which key elements of basic biology are still emerging. Using genomics and microscopy, we found that members of the bacterial lineage Planctomycetes may be central players in a subset of a freshwater lake microbiome that includes other bacteria, archaea, viruses, and mysterious entities, called aster-like nanoparticles (ALNs), whose origin is unknown. Our results help constrain the possible origins of ALNs and provide insight into possible interactions within a complex lake ecosystem.

In freshwater environments, limited data exist on the impact of mortality forces (viruses and heterotrophic nanoflagellates) on bacterial growth efficiency (BGE, index of bacterial carbon metabolism) compared to resource availability. An investigation to determine the relative influence of viral lysis and flagellate predation (top-down forces) on BGE was conducted in a mesotrophic freshwater system (Lake Goule, France) with time and space. Viral abundance was significantly (p < 0.001) related to bacterial abundance by a power law function with an exponent less than 1, emphasizing that the increases in host population (bacteria) together with viruses were not proportionate. A lytic viral strategy was evident throughout the study period, with high lysis of the bacterial population (up to 60%) supported by viral production rates. Viral processes (lysis and production) that were influenced by bacterial production and heterotrophic nanoflagellate abundance had a positive impact on BGE. Estimates of BGE were variable (9.9−45.5%) due to uncoupling between two metabolic parameters—namely bacterial production and respiration. The existence of a synergistic relationship between viruses and flagellates with bacteria in Lake Goule highlighted the decisive impact of top-down agents in sustaining the bacterial carbon metabolism of non-infected population through the nature of vital resources released via mortality processes.

The study highlights the presence of pathogenic strains of microorganisms in two swimming pools, highly frequented in the city of Yaounde. Thus, the water samples from these swimming pools have undergone physicochemical and biological treatments using conventional techniques. Three groups of microorganisms (Bacteria, Protozoa, and Helminths) were identified and quantified in these swimming pools with weakly acidic waters (6.79 ± 0.35) with an average temperature of 26.63 ± 0.53 °C and suspended matter ranging from 2 to 150 mg.l -1 . The total bacterial load varies between 8 × 10 3 and 6000 × 10 3 CFU/100 ml. It consists of mesophilic aerobic heterotrophic bacteria, fecal coliforms, total coliforms, fecal streptococci, Staphylococcus aureus, and Pseudomonas aeruginosa. Protozoan cysts and oocysts range from 122 to 505 per liter of water. These values are slightly lower for helminth eggs and larvae (0 to 108 eggs and larvae/l). In both swimming pools, significant correlations were observed between some abiotic and biotic parameters. The waters of the studied swimming pools are subject to fecal pollution. Swimmers would therefore be exposed to biological contaminations, responsible for pathologies. The most common diseases are linked to gastroenteritis (diarrhea), but infections of all kinds may be overgrown (conjunctivitis, ear infections, dermatitis, respiratory infections).

Aster-like nanoparticles (ALNs) are newly described femto-entities. Their ecology (e.g., geographic distribution, spatial dynamic, preferences, forcing factors) is still unknown. Here, we report that these entities, which have largely been ignored until now, can develop or maintain themselves in most aquatic environments in the Loire River catchment, France. We observed a significant influence of the trophic state on ALN ecological distributions. A positive relationship between prokaryotic abundance and ALN (r 2  = 0.72, p < 0.01) has been identified, but its exact nature remains to be clarified. Combined with their ubiquitous distribution and high abundances (up to 7.9 × 10 6  ALNs mL -1 ) recorded in our samples, this probably makes ALNs an overlooked functional component in aquatic ecosystems.

Since the discovery of high abundances of virus-like particles in aquatic environment, emergence of new analytical methods in microscopy and molecular biology has allowed significant advances in the characterization of the femtoplankton, i.e., floating entities filterable on a 0.2 µm pore size filter. The successive evidences in the last decade (2010-2020) of high abundances of biomimetic mineral-organic particles, extracellular vesicles, CPR/DPANN (Candidate phyla radiation/Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaeota), and very recently of aster-like nanoparticles (ALNs), show that aquatic ecosystems form a huge reservoir of unidentified and overlooked femtoplankton entities. The purpose of this review is to highlight this unsuspected diversity. Herein, we focus on the origin, composition and the ecological potentials of organic femtoplankton entities. Particular emphasis is given to the most recently discovered ALNs. All the entities described are displayed in an evolutionary context along a continuum of complexity, from minerals to cell-like living entities.

Network analyses applied to models of complex systems generally contain at least three levels of analyses. Whole-network metrics summarize general organizational features (properties or relationships) of the entire network, while node-level metrics summarize similar organization features but consider individual nodes. The network- and node-level metrics build upon the primary pairwise relationships in the model. As with many analyses, sometimes there are interesting differences at one level that disappear in the summary at another level of analysis. We illustrate this phenomenon with ecosystem network models, where nodes are trophic compartments and pairwise relationships are flows of organic carbon, such as when a predator eats a prey. For this demonstration, we analysed a time-series of 16 models of a lake planktonic food web that describes carbon exchanges within an autumn cyanobacteria bloom and compared the ecological conclusions drawn from the three levels of analysis based on inter-time-step comparisons. A general pattern in our analyses was that the closer the levels are in hierarchy (node versus network, or flow versus node level), the more they tend to align in their conclusions. Our analyses suggest that selecting the appropriate level of analysis, and above all regularly using multiple levels, may be a critical analytical decision. This article is part of the theme issue 'Unifying the essential concepts of biological networks: biological insights and philosophical foundations'.

Limited data exist on the simultaneous impact of bottom-up (nutrients) and top-down (viruses and heterotrophic nanoflagellates) forces in shaping freshwater bacterial communities. In our laboratory microcosms, nutrient additions (organic and inorganic) and viral reduction approach led to the proliferation of high nucleic acid (HNA) bacterial subpopulation without an increase in phage abundance. High viral-mediated bacterial lysis in the presence of nanoflagellates yielded high proportion of low nucleic acid bacterial subpopulation. 16S rRNA gene sequence analysis indicated that members of classes Proteobacteria and Bacteroidetes evoked differential responses to nutrients and mortality forces, thereby resulting in differences (P < 0.001) in bacterial community composition and diversity, as observed from analysis of similarities and UniFrac analysis. Bacterial species richness (Chao) and diversity (Shannon) index was significantly higher (P < 0.001) in the presence of both the top-down factors and viruses alone, whereas lower host diversity was observed under nutrient relaxation of growth-limiting substrates due to the explosive growth of opportunistic HNA bacterial subpopulation. Our results are in agreement with the theoretical model of 'killing the winner', where the availability of growth-limiting substrates can act as a stimulating factor for host community composition while top-down forces can operate in the control of host diversity., (© FEMS 2020.)

Over millennia, life has been exposed to ionizing radiation from cosmic rays and natural radioisotopes. Biological experiments in underground laboratories have recently demonstrated that the contemporary terrestrial radiation background impacts the physiology of living organisms, yet the evolutionary consequences of this biological stress have not been investigated. Explaining the mechanisms that give rise to the results of underground biological experiments remains difficult, and it has been speculated that hereditary mechanisms may be involved. Here, we have used evolution experiments in standard and very low-radiation backgrounds to demonstrate that environmental ionizing radiation does not significantly impact the evolutionary trajectories of E. coli bacterial populations in a 500 generations evolution experiment.

This study reports the discovery of Aster-Like Nanoparticles (ALNs) in pelagic environments. ALNs are pleomorphic, with three dominant morphotypes which do not fit into any previously defined environmental entities [i.e., ultramicro-prokaryotes, controversed nanobes, and non-living particles (biomimetic mineralo-organic particles, natural nanoparticles or viruses)] of similar size. Elemental composition and selected-area electron diffraction patterns suggested that the organic nature of ALNs may prevail over the possibility of crystal structures. Likewise, recorded changes in ALN numbers in the absence of cells are at odds with an affiliation to until now described viral particles. ALN abundances showed marked seasonal dynamics in the lakewater, with maximal values (up to 9.0 ± 0.5 × 10 7 particles·mL -1 ) reaching eight times those obtained for prokaryotes, and representing up to about 40% of the abundances of virus-like particles. We conclude that (i) aquatic ecosystems are reservoirs of novel, abundant, and dynamic aster-like nanoparticles, (ii) not all virus-like particles observed in aquatic systems are necessarily viruses, and (iii) there may be several types of other ultra-small particles in natural waters that are currently unknown but potentially ecologically important., (Copyright © 2019 Colombet, Billard, Viguès, Balor, Boulé, Geay, Benzerara, Menguy, Ilango, Fuster, Enault, Bardot, Gautier, Pradeep Ram and Sime-Ngando.)

The diversity of archaeal viruses is severely undersampled compared with that of viruses infecting bacteria and eukaryotes, limiting our understanding on their evolution and environmental impacts. Here, we describe the isolation and characterization of four new viruses infecting halophilic archaea from the saline Lake Retba, located close to Dakar on the coast of Senegal. Three of the viruses, HRPV10, HRPV11 and HRPV12, have enveloped pleomorphic virions and should belong to the family Pleolipoviridae, whereas the forth virus, HFTV1, has an icosahedral capsid and a long non-contractile tail, typical of bacterial and archaeal members of the order Caudovirales. Comparative genomic and phylogenomic analyses place HRPV10, HRPV11 and HRPV12 into the genus Betapleolipovirus, whereas HFTV1 appears to be most closely related to the unclassified Halorubrum virus HRTV-4. Differently from HRTV-4, HFTV1 encodes host-derived minichromosome maintenance helicase and PCNA homologues, which are likely to orchestrate its genome replication. HFTV1, the first archaeal virus isolated on a Haloferax strain, could also infect Halorubrum sp., albeit with an eightfold lower efficiency, whereas pleolipoviruses nearly exclusively infected autochthonous Halorubrum strains. Mapping of the metagenomic sequences from this environment to the genomes of isolated haloarchaeal viruses showed that these known viruses are underrepresented in the available viromes., (© 2019 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Sociality has brought many advantages to various hymenoptera species, including their ability of regulating physical factors in their nest (e.g., temperature). Although less studied, humidity is known to be important for egg, larval and pupal development, and also for nectar concentration. Two subspecies of Apis mellifera of the M evolutionary lineage were used as models to test the ability of a superorganism (i.e. honeybee colony) to regulate the humidity in its nest (i.e. "hygroregulation hypothesis") in four conservation centers: two in France (A. m. mellifera) and two in Portugal (A. m. iberiensis). We investigated the ability of both subspecies to regulate the humidity in hives daily, but also during the seasons for one complete year. Our data and statistical analysis demonstrated the capacity of the bees to regulate humidity in their hive, regardless of the day, season or subspecies. Furthermore, the study showed that humidity in beehives is stable even during winter, when brood is absent, and when temperature is known to be less stable in the beehives. These results suggest that humidity is important for honeybees at every life stage, maybe because of the 'imprint' of the evolutionary history of this hymenopteran lineage., Competing Interests: The authors have declared that no competing interests exist.

Parasitic Chytridiomycota (chytrids) are ecologically significant in various aquatic ecosystems, notably through their roles in controlling bloom-forming phytoplankton populations and in facilitating the transfer of nutrients from inedible algae to higher trophic levels. The diversity and study of these obligate parasites, while critical to understand the interactions between pathogens and their hosts in the environment, have been hindered by challenges inherent to their isolation and stable long-term maintenance under laboratory conditions. Here, we isolated an obligate chytrid parasite (CCAP 4086/1) on the freshwater bloom-forming diatom Asterionella formosa and characterized its infectious cycle under controlled conditions. Phylogenetic analyses based on 18S, 5.8S, and 28S ribosomal DNAs (rDNAs) revealed that this strain belongs to the recently described clade SW-I within the Lobulomycetales. All morphological features observed agree with the description of the known Asterionella parasite Zygorhizidium affluens Canter. We thus provide a phylogenetic placement for this chytrid and present a robust and simple assay that assesses both the infection success and the viability of the host. We also validate a cryopreservation method for stable and cost-effective long-term storage and demonstrate its recovery after thawing. All the above-mentioned tools establish a new gold standard for the isolation and long-term preservation of parasitic aquatic chytrids, thus opening new perspectives to investigate the diversity of these organisms and their physiology in a controlled laboratory environment. IMPORTANCE Despite their ecological relevance, parasitic aquatic chytrids are understudied, especially due to the challenges associated with their isolation and maintenance in culture. Here we isolated and established a culture of a chytrid parasite infecting the bloom-forming freshwater diatom Asterionella formosa The chytrid morphology suggests that it corresponds to the Asterionella parasite known as Zygorhizidium affluens The phylogenetic reconstruction in the present study supports the hypothesis that our Z. affluens isolate belongs to the order Lobulomycetales and clusters within the novel clade SW-I. We also validate a cryopreservation method for stable and cost-effective long-term storage of parasitic chytrids of phytoplankton. The establishment of a monoclonal pathosystem in culture and its successful cryopreservation opens the way to further investigate this ecologically relevant parasitic interaction., (Copyright © 2018 American Society for Microbiology.)

Though microbial processes in the oxygen minimum zones (OMZs) of the Arabian Sea (AS) are well documented, prokaryote-virus interactions are less known. The present study was carried out to determine the potential physico-chemical factors influencing viral abundances and their life strategies (lytic and lysogenic) along the vertical gradient in the OMZ of the AS (southwest coast of India). Water samples were collected during the southwest monsoon (SWM) season in two consecutive years (2015 and 2016) from different depths, namely, the surface layer, secondary chlorophyll a maxima (~30⁻40 m), oxycline (~70⁻80 m), and hypoxic/suboxic layers (~200⁻350 m). The high viral abundances observed in oxygenated surface waters (mean ± SD = 6.1 ± 3.4 × 10⁶ viral-like particles (VLPs) mL -1 ), drastically decreased with depth in the oxycline region (1.2 ± 0.5 × 10⁶ VLPs mL -1 ) and hypoxic/suboxic waters (0.3 ± 0.3 × 10⁶ VLPs mL -1 ). Virus to prokaryote ratio fluctuated in the mixed layer (~10) and declined significantly ( p < 0.001) to 1 in the hypoxic layer. Viral production (VP) and frequency of virus infected cells (FIC) were maximum in the surface and minimum in the oxycline layer, whereas the viral lysis was undetectable in the suboxic/hypoxic layer. The detection of a high percentage of lysogeny in suboxic (48%) and oxycline zones (9⁻24%), accompanied by undetectable rates of lytic viral infection support the hypothesis that lysogeny may represent the major survival strategy for viruses in unproductive or harsh nutrient/host conditions in deoxygenated waters.

We examined the relationship between viruses and co-occurring bacterial communities across spatiotemporal scale in two contrasting freshwater lakes, namely meromictic Lake Pavin and dimictic Lake Aydat (Central France). Next-generation sequencing of 16S rRNA genes suggested distinct patterns in bacterioplankton community composition (BCC) between the lakes over depths and seasons. BCC were generally dominated by members of Actinobacteria, Proteobacteria, and Bacteroidetes covering about 95% of all sequences. Oxygen depletion at the bottom waters in Aydat and existence of permanent anoxia in the monimolimnion of Pavin resulted in the occurrence and dominance of lesser known members of lake communities such as Methylotenera, Methylobacter, Gallionella, Sulfurimonas, and Syntrophus in Pavin and Methylotenera and Sulfuritalea in Aydat. Differences in BCC appeared strongly related to dissolved oxygen concentration, temperature, viral infection, and virus-to-bacteria ratio. UniFrac analysis indicated a clear distinction in BCC when the percentage of viral infected bacterial cells and virus-to-bacteria ratio exceeded a threshold level of 10% and 5, respectively, suggesting a link between viruses and their potential bacterial host communities. Our study revealed that in both the lakes, the prevailing environmental factors across time and space structured and influenced the adaptation of bacterial communities to specific ecological niches.

Parasites exist in every ecosystem and can have large influence on food web structure and function, yet, we know little about parasites' effect on food web dynamics. Here we investigate the role of microbial parasitism (viruses of bacteria, phytoplankton and cyanobacteria, and parasitic chytrids on cyanobacteria) on the dynamics of trophic pathways and food web functioning during a cyanobacteria bloom, using linear inverse food web modeling parameterized with a 2-month long data set (biomasses, infection parameters, etc.). We show the importance of grazing on heterotrophic bacteria (the microbial pathway: DOC → bacteria → consumer) and how consumers depended on bacteria during peak-cyanobacteria bloom, which abundance was partly driven by the viral activity. As bacteria become the main energy pathway to the consumers, the system takes a more web-like structure through increased omnivory, and may thereby facilitate the system's persistence to the cyanobacteria outbreak. We also showed how the killing of cyanobacteria host cells by chytrids had important impact on the food web dynamics by facilitating grazing on the cyanobacteria, and by offering alternative pathways to the consumers. This seemed to increase the system's ability to return to a mix of trophic pathways, which theoretically increases the stability of the system.

Bacteria assemblages in lake sediments play a key role in various biogeochemical processes, yet their association with interstitial pore waters has been scarcely investigated. In this study, we utilized Illumina next-generation amplicon sequencing of the 16S rRNA gene to characterize the seasonal bacterial communities in the sediments and pore waters of three contrasted temperate freshwater lakes, namely Pavin, Aydat, and Grangent (French Massif Central). Despite occupying seemingly similar habitats, bacterial communities differed substantially between sediments and pore waters at all seasons with low sharing of operational taxonomic units (OTUs, 6.7 to 20.3%) between them. Sediment-associated bacteria were more rich and diverse than pore water bacteria, indicating a high heterogeneity in the sediment microhabitat. The changes in both sediment and pore water bacterial communities were lake and season specific. The bacterial community showed distinct differences between the lakes, with larger presence of strict anaerobes such as Syntrophus, Syntrophorhabdus, and Sulfuricurvum in the pore water and sediments of Pavin responsible for carbon and sulfur cycling. In both Aydat and Grangent, the hgcI&#95;clade dominated throughout the study period in the pore waters. The higher representation of lesser-known transient members of lake communities such as Methylotenera in the pore waters of Aydat, and Clostridium and Sulfuricurvum in the pore and sediments of Grangent, respectively, were observed during the period of temporary anoxia in summer caused by lake stratification. Our study revealed that in the investigated lakes, the prevailing environmental factors across time and space structured and influenced the adaptation of bacterial communities to specific ecological niches.

Our understanding on the importance of viral lysis in the functioning of tropical estuarine ecosystem is limited. This study examines viral infection of prokaryotes and subsequent lysis of cells belonging to different morphotypes across a salinity gradient in monsoon driven estuarine ecosystem (Cochin estuary, India). High standing stock of viruses and prokaryotes accompanied by lytic infection rates in the euryhaline/mesohaline region of the estuary suggests salinity to have an influential role in driving interactions between prokaryotes and viruses. High prokaryotic mortality rates, up to 42% of prokaryote population in the pre-monsoon season is further substantiated by a high virus to prokaryote ratio (VPR), suggesting that maintenance of a high number of viruses is dependent on the most active fraction of bacterioplankton. Although myoviruses were the dominant viral morphotype (mean = 43%) throughout the study period, there was significant variation among prokaryotic morphotypes susceptible to viral infection. Among them, the viral infected short rod prokaryote morphotype with lower burst estimates (mean = 18 viruses prokaryote-1) was dominant (35%) in the dry seasons whereas a substantial increase in cocci forms (30%) infected by viruses with high burst size (mean = 31 viruses prokaryote-1) was evident during the monsoon season. Such preferential infections of prokaryotic morphopopulations with respect to seasons can have a strong and variable impact on the carbon and energy flow in this tropical ecosystem.

Morphological and infraciliature studies carried out using pyridinated ammoniacal silver carbonate and the 4',6-diamidino-2-phenylindole (DAPI) staining techniques, led to the identification of two new species of ciliates pertaining to the subclass Astomatia. The first species, Hoplitophrya polymorphus sp. nov., displays two main cellular forms: the elongated form (150-247 μm long and 40-87 μm width) and the stocky form (140-170 μm long and 70-98 μm width). The macronucleus is generally skinny in the elongated forms and ribbon-shaped in the stocky forms. The common feature of the two cellular shapes uniting them in the same species is the identical structure of their skeletal apparatus, a V-shaped element located in an apical depression and bearing skeletal fibres on its ventral face. The second species, Anoplophrya simplex sp. nov., is totally deprived of skeletal apparatus. The cell shape is fusiform and dorsoventrally flattened (105-180 μm long and 65-125 μm width). Six to 12 pulsatile vacuoles form two rows arranged symmetrically on either side of the macronucleus. These two newly identified species highlight the extremely rich diversity of ciliates inhabiting the digestive tract of tropical earthworms.

The significance of lytic viral lysis in shaping bacterial communities in temperate freshwater systems is less documented. Here we used Illumina sequencing of 16S rRNA genes to examine bacterial community structure and diversity in relation to variable viral lysis in the euphotic zone of 25 temperate freshwater lakes (French Massif Central). We captured a rich bacterial community that was dominated by a few bacterial classes and operational taxonomic units (OTUs) frequently detected in other freshwater ecosystems. In the investigated lakes with contrasting physico-chemical characteristics, the dominant bacterioplankton community was represented by major taxonomical orders, namely Actinomycetales, Burkholderiales, Sphingobacteriales, Acidimicrobiales, Flavobacteriales and Cytophagales covering about 70% of all sequences. Viral lysis was significantly correlated with the bacterial diversity indices (Chao, Shannon, OTUs) which explained about 33% and 45% of the variation in species diversity and observed richness respectively. Anosim and UniFrac analyses indicated a clear distinction of bacterial community structure among the lakes that exhibited high and low lytic viral infection (FIC) rates. Based on our findings, high FIC (>10%) supported higher species richness, whereas low FIC (<10%) resulted in less diverse community. Our study strongly suggests that lytic activity prevailed over the type of lake ecosystems in shaping bacterioplankton diversity., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Chytridiomycota, often referred to as chytrids, can be virulent parasites with the potential to inflict mass mortalities on hosts, causing e.g. changes in phytoplankton size distributions and succession, and the delay or suppression of bloom events. Molecular environmental surveys have revealed an unexpectedly large diversity of chytrids across a wide range of aquatic ecosystems worldwide. As a result, scientific interest towards fungal parasites of phytoplankton has been gaining momentum in the past few years. Yet, we still know little about the ecology of chytrids, their life cycles, phylogeny, host specificity and range. Information on the contribution of chytrids to trophic interactions, as well as co-evolutionary feedbacks of fungal parasitism on host populations is also limited. This paper synthesizes ideas stressing the multifaceted biological relevance of phytoplankton chytridiomycosis, resulting from discussions among an international team of chytrid researchers. It presents our view on the most pressing research needs for promoting the integration of chytrid fungi into aquatic ecology., (© 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.)

Parasitism is certainly one of the most important driving biotic factors of cyanobacterial blooms which remains largely understudied. Among these parasites, fungi from the phylum Chytridiomycota (i.e. chytrids) are the only eukaryotic microorganisms infecting cyanobacteria. Here, we address spatiotemporal dynamics of the cyanobacterial host Dolichospermum macrosporum (syn. Anabaena macrospora) and its associated chytrid parasites, Rhizosiphon spp., in an eutrophic lake by studying spatial (vertical, horizontal) and temporal (annual and inter-annual) variations. Our results show homogenous chytrid infection patterns along the water column and across sampling stations. However, the prevalence of infection presented drastic changes with time, at both intra- and inter-annual scales. In 2007, a maximum of 98% of vegetative cells were infected by R. crassum whereas this fungal species was not reported seven years later. In opposite, R. akinetum, a chytrid infecting only akinetes, increased its prevalence by 42% during the same period. High chytrid infection rate on the akinetes might have sizeable consequences on host recruitment (and proliferation) success from year to year, as supported by the recorded inter-annual host dynamics (affecting also the success of other chytrid parasites). The spatial homogenous chytrid infection on this cyanobacterium, coupled to both seasonal and inter-annual changes indicates that time, rather than space, controls such highly dynamic host-parasite relationships.

Biological experiments conducted in underground laboratories over the last decade have shown that life can respond to relatively small changes in the radiation background in unconventional ways. Rapid changes in cell growth, indicative of hormetic behaviour and long-term inheritable changes in antioxidant regulation have been observed in response to changes in the radiation background that should be almost undetectable to cells. Here, we summarize the recent body of underground experiments conducted to date, and outline potential mechanisms (such as cell signalling, DNA repair and antioxidant regulation) that could mediate the response of cells to low radiation backgrounds. We highlight how multigenerational studies drawing on methods well established in studying evolutionary biology are well suited for elucidating these mechanisms, especially given these changes may be mediated by epigenetic pathways. Controlled evolution experiments with model organisms, conducted in underground laboratories, can highlight the short- and long-term differences in how extremely low-dose radiation environments affect living systems, shining light on the extent to which epimutations caused by the radiation background propagate through the population. Such studies can provide a baseline for understanding the evolutionary responses of microorganisms to ionizing radiation, and provide clues for understanding the higher radiation environments around uranium mines and nuclear disaster zones, as well as those inside nuclear reactors.

Viruses are recognized as the most abundant and dynamic biological entities in the marine and estuarine environment. However, studies on the dynamics and activity of viruses in transient estuarine systems are limited. This study examines temporal and spatial variations in viral abundance (VA) and viral activity across the salinity gradient in a monsoon-driven tropical estuarine system (Cochin estuary, CE) along the southwest coast of India. Water samples were collected from five stations (with different hydrological settings) every 3 h for 24 h period during two distinct seasons, namely pre-monsoon (PRM, dry season) and monsoon (MON, wet season). Time series measurements were made for a spring and neap tidal cycle for each season at all the stations. The results showed marked spatial and seasonal variability with relatively low diel and tidal variations in VA and lytic activity. Viral activity was found to be distinct in five stations studied with the maximum activity in the mesohaline regions (salinity <20) of the estuary. This region was characterized by high VA, lytic infection and viral production, accompanied by low (BGE) and high bacterial respiration. Based on viral lytic production, lytic viruses were found to be responsible for the release of ca. 72.9 ± 58.5 μg C L -1 d -1 of bacterial carbon. The contribution of the viral shunt to the dissolved organic carbon (DOC) pool was higher during the dry season (PRM) than MON. Statistical analysis confirmed a significant association of viruses with the host availability and salinity. This work demonstrates the spatiotemporal distribution of viruses in a tropical estuarine ecosystem and highlights their role in microbial mortality across different salinity gradients. This study forms the first report on viral processes from a monsoon-driven tropical estuarine ecosystem.

We examined changes in morphological and genomic diversities of viruses by means of transmission electronic microscopy and pulsed field gel electrophoresis (PFGE) over a nine-month period (April-December 2005) at four different depths in the oligomesotrophic Lac Pavin. We found that the majority of viruses in this lake belonged to the family of Siphoviridae or were untailed, with capsid sizes ranging from 30 to 60nm, and exhibited genome sizes ranging from 15 to 45kb. On average, 12 different genotypes dominated each of the PFGE fingerprints. The highest genomic viral richness was recorded in summer (mean=14 bands per PFGE fingerprint) and in the epilimnion (mean=13 bands per PFGE fingerprint). Among the physico-chemical and biological variables considered, the availability of the hosts appeared to be the main factor regulating the variations in the viral diversity., (Copyright © 2016. Published by Elsevier B.V.)

Microbial diversity provides an immense reservoir of functions and supports key steps in maintaining ecosystem balance through matter decomposition processes and nutrient recycling. The use of microorganisms for biomolecule production is now common, but often involves single-strain cultures. In this review, we highlight the significance of using ecosystem-derived microbial diversity for biotechnological researches. In the context of organic matter mineralization, diversity of microorganisms is essential and enhances the degradation processes. We focus on anaerobic production of biomolecules of interest from discarded biomass, which is an important issue in the context of organic waste valorization and processing. Organic waste represents an important and renewable raw material but remains underused. It is commonly accepted that anaerobic mineralization of organic waste allows the production of diverse interesting molecules within several fields of application. We provide evidence that complex and diversified microbial communities isolated from ecosystems, i.e. microbial consortia, offer considerable advantages in degrading complex organic waste, to yield biomolecules of interest. We defend our opinion that this approach is more efficient and offers enhanced potential compared to the approaches that use single strain cultures.

We conducted an experimental approach using microcosms to simultaneously examine the functional response of natural freshwater bacterial assemblages to the impact of resources (nutrients) and top-down factors (viruses and grazers) on bacterial physiological state and their community structure. Addition of organic and inorganic nutrients led to the proliferation of high nucleic acid content bacterial cells accompanied by high bacterial growth efficiency (considered as proxy of bacterial carbon metabolism) estimates, suggesting that this subgroup represented the most active fraction of bacterial community and had a high capacity to incorporate carbon into its biomass. However, their rapid growth induced the pressure of viral lytic infection which led to their lysis toward the end of the experiment. In microcosms with flagellates plus viruses, and with viruses alone, the selective removal of metabolically active high nucleic acid cells through viral lysis benefitted the less active low nucleic acid content cells, perhaps via the use of lysis products for its growth and survival. Changes in bacterial physiological state in microcosms were reflected in their community structure which was examined using 16S ribosomal RNA (rRNA) gene sequencing by Illumina's Miseq platform. Chao estimator and Shannon diversity index values suggested that bacterial species richness was highest in the presence of both the top-down factors, indicating a tighter control of bacterioplankton dominants within a relatively stable bacterial community. The increase in bacterial metabolism with nutrient addition followed by subsequent lysis of bacterial dominants indicate that both resources and top-down factors work in concert for the sustenance of stable bacterial communities.