Editorial for the special issue: Gut microorganisms of aquatic animals

[No abstract available

Advancing knowledge on cyanobacterial blooms in freshwaters

Cyanobacterial blooms have become a frequent phenomenon in freshwaters worldwide; they are a widely known indicator of eutrophication and water quality deterioration. Information and knowledge contributing towards the evaluation of the ecological status of freshwaters, particularly since many are used for recreation, drinking water, and aquaculture, is valuable. This Special Issue, entitled "Advancing Knowledge on Cyanobacterial Blooms in Freshwaters", includes 11 research papers that will focus on the use of complementary approaches, from the most recently developed molecular-based methods to more classical approaches and experimental and mathematical modelling regarding the factors (abiotic and/or biotic) that control the diversity of not only the key bloom-forming cyanobacterial species, but also their interactions with other biota, either in freshwater systems or their adjacent habitats, and their role in preventing and/or promoting cyanobacterial growth and toxin production. © 2020 by the authors

Variability of prokaryotic community structure in a drinking water reservoir (Marathonas, Greece)

The structure of the Bacteria and Archaea community in a large drinking water reservoir (Marathonas, Greece; MR) was investigated in October 2007 and September 2008, using 16S rRNA gene clone libraries. The bacterial communities were more diverse than archaeal communities (Shannon diversity index H' 0.81-3.28 and 1.36-1.77, respectively). The overall bacterial community composition was comparable to bacterioplankton community described in other freshwater habitats. Within the Bacteria, Betaproteobacteria dominated, while representatives of Alpha-, Gamma- and Deltaproteobacteria also occurred. Other important phyla were Actinobacteria and Bacteroidetes, while representatives of Acidobacteria, Cyanobacteria, Chloroflexi, Planctomycetes and Verrucomicrobia were also retrieved. Several phylotypes in Alpha- and Betaproteobacteria and Bacteroidetes were related to bacteria capable of cyanotoxin degradation and with aromatic compounds/iron oxidizers or polymer degraders. Euryarchaeota dominated (60.5%) the Archaea community mostly with phylotypes related to Methanobacteriales and Methanosarcinales. Among the Thaumarchaeota, the two most abundant phylotypes were affiliated (97% similarity) with the only cultivated mesophilic thaumarchaeote of marine origin, Nitrosopumilus maritimus. Temporal and spatial comparison of the prokaryotic community structure revealed that three of the most abundant prokaryotic phylotypes, belonging to Actinobacteria, were recovered from all sites both years, suggesting that these Actinobacteria could be important key players in MR ecosystem functioning

Size-fractionated phytoplankton chlorophyll in an Eastern Mediterranean coastal system (Maliakos Gulf, Greece)

The dynamics of phytoplankton biomass were studied in an Eastern Mediterranean semi-enclosed coastal system (Maliakos Gulf, Aegean Sea), over 1 year. In particular, chlorophyll a (chl a) was fractionated into four size classes: Picoplankton (0.2-2 μm), nanoplankton (2-20 μm), microplankton (20-180 μ) and net phytoplankton (>180 μm). The spatial and temporal variation in dissolved inorganic nutrients and particulate organic carbon (POC) were also investigated. The water column was well mixed throughout the year, resulting in no differences between depths for all the measured parameters. Total chl a was highest in the inner part of the gulf and peaked in winter (2.65 μg 1-1). During the phytoplankton bloom, microplankton and net phytoplankton together dominated the autotrophic biomass (67.2-95.0% of total chl a), while in the warmer months the contribution of pico- and nanoplankton was the most significant (77.5-93.4% of total chl a). The small fractions, although showing low chl a concentrations, were important contributors to the POC pool, especially in the outer gulf. No statistically significant correlations were found between any chl a size fraction and inorganic nutrients. For most of the year, phytoplankton was not limited by inorganic nitrogen concentrations

A non-phylogenetic alpha diversity approach on prokaryotic community structure in aquatic systems

Comparative analyses of accumulating phylotype-abundance data of prokaryotic communities are relatively scarce and mainly approached with phylogenetic methodologies. However, when a great fraction of phylotypes is captured within a sample, application of alpha diversity measures is also possible, enabling the exploration of structural changes in prokaryotic communities. In the present study, phylotype-abundance data of Archaea and Bacteria were compiled from previous works on freshwater, thermal springs, and submarine mud volcanoes in Eastern Mediterranean region. Samples within each environment were used as pseudo-replicates to enable comparisons between the two assemblages (Archaea and Bacteria) and among different environments whereas sampling effort was found similar among samples using rarefaction curves. Phylotypes were defined as 16S rRNA sequences with 98% similarity. The most common diversity indices were calculated and relative abundance distributions (RADs) were employed to provide a more detailed interpretation of observed diversity patterns. The freshwater and mud volcanoes environments were the most diverse with respect to Bacteria but the least diverse considering Archaea, whereas thermal springs yielded very similar diversity for both assemblages. Overall, bacterial diversity was higher than archaeal with respect to richness and evenness since Archaea were characterized by high dominance and phylotype-poor distributions. The present comparative analysis of alpha diversity may offer useful insights into ecological processes shaping prokaryotic community structure, however equal sampling effort among different environments must be verified prior to analysis

Microbiological confinement of two adjacent water wells in Lake Karla Basin, Greece

We analyzed the bacterial and archaeal community structure of two adjacent irrigation well waters of the Lake Karla Basin, Central Greece, in order to elucidate their connectivity or confinement by using 454 tag pyrosequencing of the 16S rRNA genes. Although considerable overlap was found at the phylum/high taxonomic level, and also at the operational taxonomic units (OTU) level, the dominant, and most likely active, prokaryotes represented by these OTUs were very different between the two wells. As expected, we found higher bacterial species richness compared to that of archaeal, and this renders Bacteria better for the study of connectivity or confinement of water wells. Some of the taxonomic groups found are amongst those found typically in the terrestrial subsurface and also those that have been recently described, enhancing the importance of the subsurface for expanding our knowledge on microbial diversity. The majority of the archaeal and several of the bacterial OTUs, including the most dominant ones in each well, were related to marine or saline environments, indicating the previously suggested persistence of fertilizer residuals in the basin's soils. © 2015 by the authors

Prokaryotic diversity in marine and freshwater recirculating aquaculture systems

Intensive aquaculture food production has been continually increasing over the past decades. Recirculating aquaculture is an innovative technology which relies on water reuse and removal of toxic metabolites by utilizing specific prokaryotic groups such as nitrifiers, settled in special biofilters. Focused on recent next generation sequencing-based studies on the microbiome of recirculating aquaculture systems, this review highlights dominant genera and families, and investigates their possible metabolic function in key niches within recirculating aquaculture systems (rearing water, biofilters and fish mucosal microbiome), while aiming to identify core prokaryotic groups across studies. A total of 136 genera belonging to 77 families and 13 phyla have been characterized as dominant or functionally important in relevant studies, mainly isolated from nitrification biofilters, system water and intestinal samples of the farmed species. Proteobacteria is undoubtedly the most abundant phylum, followed by Bacteroidetes, Firmicutes and Actinobacteria, while Rhodobacteriaceae and Flavobacteriaceae are the common dominant families. Nitrosomonadaceae and Nitrospira members are enriched in biofilter samples and serve as the most common ammonium and nitrite oxidizers, respectively. Composition of dominant genera appears system specific due to unique characteristics of individual RAS designs, although faint community patterns emerge when examining RAS by their salinity level. Considering the number of ribosomal RNA operon copies, 75% of genera are likely slow growers, dominating biofilter and water communities, whereas the few fast-growing opportunists are mainly associated with the intestine of farmed species. Finally, this review stresses the lack of information regarding archaeal and microeukaryotic communities in recirculating aquaculture systems and prokaryotic–protist interactions. © 2022 John Wiley & Sons Australia, Ltd

Editorial: Microbial Communities of Coastal Eutrophic Systems

[No abstract available

Temporal variations of nutrients, chlorophyll a and particulate matter in three coastal lagoons of Amvrakikos Gulf (Ionian Sea, Greece)

The temporal variations of nutrients, chlorophyll a (chl a), suspended particulate matter (SPM) and particulate organic carbon (POC) were measured over 12 months in three shallow coastal brackish water lagoons of the Amvrakikos Gulf, Ionian Sea. Two of the lagoons, Tsoukalio and Rodia, are interconnected but separated from Logarou by a narrow strip of land. Logarou has a better water exchange with the sea as indicated by the higher salinity and dissolved oxygen concentrations and the smaller variation of the above-mentioned parameters. Nitrate concentrations were largely the same in the three lagoons and higher than in the Amvrakikos Gulf. Phosphate concentrations in Logarou exceeded by far those of Tsoukalio/Rodia; the increased phosphate levels recorded in January caused an extended phytoplankton bloom with chl a concentrations higher than in the other two lagoons. Chl a in Tsoukalio was positively correlated with nitrate whereas in the most shallow lagoon, Logarou, it showed a positive correlation with light winds (force 4 and lower), probably caused by resuspension from the sediment. Increased phytoplankton biomass in Logarou coupled with the better water exchange may be related to the higher fish production in this lagoon

Inter-annual variability of soft bottom macrofaunal communities in two Ionian Sea lagoons

Inter-annual variation in the composition of the soft bottom macrobenthic communities of two undisturbed lagoons, in Amvrakikos Gulf, Ionian Sea, Greece, was investigated over three consecutive summers. The environmental parameters that showed the greatest variability were organic carbon of the sediment and salinity. The species found were typical of lagoonal systems, the most common and abundant of which were Abra ovata, Mytilaster minimus and, in the most enclosed areas, larvae of chironomids. Multivariate analysis registered community changes, which were mostly caused by changes in species dominance. Structural community characteristics such as number of species, number of individuals and diversity did not show significant differences among years except in the stations with least water exchange with the sea. © Springer 2006