Cyanobacterial blooms in lakes frequently display high spatial heterogeneity, which may drive temporal changes in microbial community structure. Here we report on the spatial (horizontal and ...vertical) structure of the cyanobacteria community and of the co‐occurring heterotroph microbial community during a major lake‐wide bloom event at Lake Kinneret (Sea of Galilee, Israel).
We sampled the upper water layer (0, 1 and 5 m depths) at five locations across the lake, spatially representing north, south, east, west and centre of the lake, on two dates during winter 2016 when the Microcystis biomass was high. We aimed to characterise the spatial distribution of the bloom and the associated microbiota, as well as testing the extent to which variation in the structure of the microbial community could be associated with Microcystis biomass.
During the winter 2016 bloom, Microcystis biomass was spatially heterogeneous, but the Microcystis population structure was rather homogenous, dominated by a single genotype (ITS sequence variant). By contrast, the composition of the bacterial community, assessed using 16S rRNA gene sequencing, was spatially heterogeneous, differing between depths, sampling locations and time.
The largest difference in microbial community structure was between particle‐associated (PA) and free‐living (FL) fractions. The PA community was characterised by a relatively lower diversity, and dominated by Proteobacteria, whereas the FL community was significantly more diverse and dominated by members of Proteobacteria, Bacteroidetes and Actinobacteria. Variation in the microbial community was significantly correlated with geographical location and sampling depth. However, there was no clear relationship between the Microcystis biomass density (cells biovolume) and the structure of the microbial communities.
These results suggest that the structure of the bacterial community is partly decoupled from Microcystis population density, and potentially more affected by other environmental factors such as temperature and/or physicochemical conditions. Our study highlights the importance of spatial information on bloom composition and intensity in clarifying the factors affecting the progression of cyanobacterial harmful algal blooms and how this impacts their microbial counterparts.
Intensive freshwater aquaculture in the Spring Valley, Israel, is implemented mainly in earthen fishponds and reservoirs that are stocked with a variety of edible fish species. Here we sampled six ...different healthy fish species from these intensive aquacultures. The fish were hybrid striped bass, European bass, red drum (all carnivores), hybrid tilapia, flathead grey mullet (both herbivores), and common carp (an omnivore). Significant differences were found among the intestinal microbiota of the six studied fish species. The microbiota composition diversity was strongly related to the trophic level of the fish, such that there was a significant difference between the carnivore and the herbivore species, while the omnivore species was not significantly different from either group. The most abundant genus in the majority of the fishes' intestinal microbiota was
. Furthermore, we found that beside
, a unique combination of taxa with relative abundance >10% characterized the intestine microbiota of each fish species: unclassified
,
, and
(hybrid striped bass);
and
1 (European bass);
(red drum);
-
(hybrid tilapia); unclassified
and unclassified
(flathead grey mullet); and
(common carp). We conclude that each fish species has a specific bacterial genera combination that characterizes it. Moreover, diet and the trophic level of the fish have a major influence on the gut microbiota of healthy fish that grow in intensive freshwater aquaculture.
Plant microbiomes are critical to host adaptation and impact plant productivity and health. Root-associated microbiomes vary by soil and host genotype, but the contribution of these factors to ...community structure and metabolic potential has not been fully addressed. Here we characterize root microbial communities of two disparate agricultural crops grown in the same natural soil in a controlled and replicated experimental system. Metagenomic (genetic potential) analysis identifies a core set of functional genes associated with root colonization in both plant hosts, and metatranscriptomic (functional expression) analysis revealed that most genes enriched in the root zones are expressed. Root colonization requires multiple functional capabilities, and these capabilities are enriched at the community level. Differences between the root-associated microbial communities from different plants are observed at the genus or species level, and are related to root-zone environmental factors.
Abstract
Symbiotic bacteria within the gut microbiome of various organisms, including fish, provide the host with several functions that improve the immune system. Although the spleen plays an ...important role in the modulation of immune responses, the role of spleen microbiota in shaping the immune system is unclear. Our study aimed at understanding the relationship between fish health and microbiota composition in the intestine and spleen. Our model organism was the hybrid tilapia (
Oreochromis aureus
×
Oreochromis niloticus
). We sampled intestine and spleen from healthy and diseased adult tilapia and determined their microbiota composition by sequencing the 16S rRNA gene. Significant differences were found between the intestine and the spleen microbiota composition of healthy compared to diseased fish as well as between intestines and spleens of fish with the same health condition. The microbiota diversity of healthy fish compared to diseased fish was significantly different as well. In the intestine of healthy fish,
Cetobacterium
was the most abundant genus while
Mycoplasma
was the most abundant genus in the spleen.
Vibrio
was the most abundant genus in the intestine and spleen of diseased fish. Moreover, it seems that there is a co-infection interaction between
Vibrio
and
Aeromonas
, which was reflected in the spleen of diseased fish. While
Vibrio, Aeromonas
and
Streptococcus
were the probable pathogens in the diseased fish, the role of
Mycoplasma
as a pathogen of cultured hybrid tilapia remains uncertain. We conclude that the intestine and spleen microbiota composition is strongly related to the health condition of the fish.
Summary
This study is an initial description and discussion of the kidney and liver microbial communities of five common fish species sampled from four sites along the Eastern Mediterranean Sea ...shoreline. The goals of the present study were to establish a baseline dataset of microbial communities associated with the tissues of wild marine fish, in order to examine species‐specific microbial characteristics and to screen for candidate pathogens. This issue is especially relevant due to the development of mariculture farms and the possible transmission of pathogens from wild to farmed fish and vice versa. Although fish were apparently healthy, 16S rRNA NGS screening identified three potential fish bacterial pathogens: Photobacterium damselae, Vibrio harveyi and Streptococcus iniae. Based on the distribution patterns and relative abundance, 16 samples were classified as potential pathogenic bacteria‐infected samples (PPBIS). Hence, PPBIS prevalence was significantly higher in kidneys than in liver samples and variation was found between the fish species. Significant differences were observed between fish species, organs and sites, indicating the importance of the environmental conditions on the fish microbiome. We applied a consistent sampling and analytical method for monitoring in long‐term surveys which may be incorporated within other marine fish pathogens surveys around the world.
This study is an initial description and discussion of the kidney and liver microbial communities of five common fish species sampled from four sites along the Eastern Mediterranean Sea shoreline. The goals of the present study were to establish a baseline dataset of microbial communities associated with the tissues of wild marine fish, in order to examine species‐specific microbial characteristics and to screen for candidate pathogens.
Ecosystem dynamics in monomictic lakes are characterized by seasonal thermal mixing and stratification. These physical processes bring about seasonal variations in nutrients and organic matter ...fluxes, affecting the biogeochemical processes that occur in the water column. Physical and chemical dynamics are generally reflected in seasonal structural changes in the phytoplankton and bacterio-plankton community. In this study, we analyzed, using 16S rRNA amplicon sequencing, the structure of the bacterial community associated with large particles (>20 μm) in Lake Kinneret (Sea of Galilee, Israel), and its associations to phytoplankton populations. The study was carried out during late winter and early spring, a highly dynamic period in terms of thermal mixing, nutrient availability, and shifts in phytoplankton composition. Structural changes in the bacterioplankton population corresponded with limnological variations in the lake. In terms of the entire heterotrophic community, the structural patterns of particle-associated bacteria were mainly correlated with abiotic factors such as pH, ammonia, water temperature and nitrate. However, analysis of microbial taxon-specific correlations with phytoplankton species revealed a strong potential link between specific bacterial populations and the presence of different phytoplankton species, such as the cyanobacterium Microcystis, as well as the dinoflagellates Peridinium and Peridiniopsis. We found that Brevundimonas, a common freshwater genus, and Bdellovibrio, a well-known Gram-negative bacteria predator, were positively associated to Microcystis, suggesting a potentially important role of these three taxa in the microbial ecology of the lake. Our results show that the dynamics of environmental abiotic conditions, rather than specific phytoplankton assemblages, are the main factors positively correlated with changes in the community structure as a whole. Nevertheless, some specific bacteria may interact and be linked with specific phytoplankton, which may potentially control the dynamic patterns of the microbial community.
Myxozoa is a unique group of obligate endoparasites in the phylum Cnidaria that can cause emerging diseases in wild and cultured fish populations. Recently, we identified a new myxozoan species, ...Myxobolus bejeranoi, which infects the gills of cultured tilapia while suppressing host immunity. To uncover the molecular mechanisms underlying this successful parasitic strategy, we conducted transcriptomics analysis of M. bejeranoi throughout the infection. Our results show that histones, which are essential for accelerated cell division, are highly expressed even one day after invasion. As the infection progressed, conserved parasitic genes that are known to modulate the host immune reaction in different parasitic taxa were upregulated. These genes included energy-related glycolytic enzymes, as well as calreticulin, proteases, and miRNA biogenesis proteins. Interestingly, myxozoan calreticulin formed a distinct phylogenetic clade apart from other cnidarians, suggesting a possible function in parasite pathogenesis. Sporogenesis was in its final stages 20 days post-exposure, as spore-specific markers were highly expressed. Lastly, we provide the first catalog of transcription factors in a Myxozoa species, which is minimized compared to free-living cnidarians and is dominated by homeodomain types. Overall, these molecular insights into myxozoan infection support the concept that parasitic strategies are a result of convergent evolution.
Advances in metagenomics enable high resolution description of complex bacterial communities in their natural environments. Consequently, conceptual approaches for community level functional analysis ...are in high need. Here, we introduce a framework for a metagenomics-based analysis of community functions. Environment-specific gene catalogs, derived from metagenomes, are processed into metabolic-network representation. By applying established ecological conventions, network-edges (metabolic functions) are assigned with taxonomic annotations according to the dominance level of specific groups. Once a function-taxonomy link is established, prediction of the impact of dominant taxa on the overall community performances is assessed by simulating removal or addition of edges (taxa associated functions). This approach is demonstrated on metagenomic data describing the microbial communities from the root environment of two crop plants - wheat and cucumber. Predictions for environment-dependent effects revealed differences between treatments (root vs. soil), corresponding to documented observations. Metabolism of specific plant exudates (e.g., organic acids, flavonoids) was linked with distinct taxonomic groups in simulated root, but not soil, environments. These dependencies point to the impact of these metabolite families as determinants of community structure. Simulations of the activity of pairwise combinations of taxonomic groups (order level) predicted the possible production of complementary metabolites. Complementation profiles allow formulating a possible metabolic role for observed co-occurrence patterns. For example, production of tryptophan-associated metabolites through complementary interactions is unique to the tryptophan-deficient cucumber root environment. Our approach enables formulation of testable predictions for species contribution to community activity and exploration of the functional outcome of structural shifts in complex bacterial communities. Understanding community-level metabolism is an essential step toward the manipulation and optimization of microbial function. Here, we introduce an analysis framework addressing three key challenges of such data: producing quantified links between taxonomy and function; contextualizing discrete functions into communal networks; and simulating environmental impact on community performances. New technologies will soon provide a high-coverage description of biotic and a-biotic aspects of complex microbial communities such as these found in gut and soil. This framework was designed to allow the integration of high-throughput metabolomic and metagenomic data toward tackling the intricate associations between community structure, community function, and metabolic inputs.
Microbial fuel cells (MFCs) generate energy while aiding the biodegradation of waste through the activity of an electroactive mixed biofilm. Metabolic cooperation is essential for MFCs' efficiency, ...especially during early colonization. Thus, examining specific ecological processes that drive the assembly of anode biofilms is highly important for shortening startup times and improving MFC performance, making this technology cost-effective and sustainable. Here, we use metagenomics to show that bioaugmentation of the anode surface with a taxonomically defined electroactive consortium, dominated by
, resulted in an extremely rapid current density generation. Conversely, the untreated anode surface resulted in a highly stochastic and slower biofilm assembly. Remarkably, an efficient anode colonization process was obtained only if wastewater was added, leading to a nearly complete replacement of the bioaugmented community by
Although different approaches to improve MFC startup have been investigated, we propose that only the combination of anode bioaugmentation with wastewater inoculation can reduce stochasticity. Such an approach provides the conditions that support the growth of specific newly arriving species that positively support the fast establishment of a highly functional anode biofilm.
Mixed microbial communities play important roles in treating wastewater, in producing renewable energy, and in the bioremediation of pollutants in contaminated environments. While these processes are well known, especially the community structure and biodiversity, how to efficiently and robustly manage microbial community assembly remains unknown. Moreover, it has been shown that a high degree of temporal variation in microbial community composition and structure often occurs even under identical environmental conditions. This heterogeneity is directly related to stochastic processes involved in microbial community organization, similarly during the initial stages of biofilm formation on surfaces. In this study, we show that anode surface pretreatment alone is not sufficient for a substantial improvement in startup times in microbial fuel cells (MFCs), as previously thought. Rather, we have discovered that the combination of applying a well-known consortium directly on the anode surface together with wastewater (including the bacteria that they contain) is the optimized management scheme. This allowed a selected colonization process by the wastewater species, which improved the functionality relative to that of untreated systems.
Ulva
is a commercially important marine macroalga. It hosts both epiphytes and endophytes. The latter are assumed to protect
Ulva
through secondary metabolites. Previously, we demonstrated bioactive ...endophytes from macroalgae with great potential to control diseases of aquaculture. In this study, we introduced a bioactive bacterial endophyte back into its original host (
Ulva
sp.) and demonstrated its survival over time in fresh and freeze-dried
Ulva
sp. We visualized the endophyte’s location and survival in the seaweed using a Green Fluorescent Protein (GFP) reporter gene. The isolate colonized the intercellular space and survived for at least 5 months in fresh, and 12 months in freeze-dried algae, while maintaining its bioactivity against the aquaculture pathogen
Streptococcus iniae
. We studied the influence of the endophyte on the bacterial community in the
Ulva
sp. We found that once introduced, the endophyte significantly changed algal microbiota diversity and abundance. Two of
Ulva
’s associated bacterial species were quantified over time, suggesting different trends in absolute abundance of these bacteria between treatments. To the best of our knowledge, this is the first report of the successful introduction of an endophytic microorganism into macroalgal tissue. These findings may be useful in applied research for the potential management of aquaculture diseases.
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