Biofouling is the main challenge in the operation of anaerobic membrane bioreactors (AnMBRs). Biofouling strongly depends on temperature; therefore, we hypothesize that the interactions and viscoelastic properties of soluble microbial products (SMP) and extracellular polymeric substances (EPS) vary with temperature, consequently influencing membrane permeability. This study compares the performance of an AnMBR operated at a similar permeate flux at two temperatures. The transmembrane pressure (TMP) rose rapidly after 5 ± 2 days at 25 °C but only after 18 ± 2 days at 35 °C, although the reactor's biological performance was similar at both temperatures, in terms of the efficiency of dissolved organic carbon removal and biogas composition, which were obtained by changing the hydraulic retention time. Using confocal laser scanning microscopy (CLSM), a higher biofilm amount was detected at 25 °C than at 35 °C, while quartz crystal microbalance with dissipation (QCM-D) showed a more adhesive, but less viscous and elastic EPS layer. In situ optical coherence tomography (OCT) of an ultra-filtration membrane, fed with the mixed liquor suspended solids (MLSS) at the two temperatures, revealed that while a higher rate of TMP increase was obtained at 25 °C, the attachment of biomass from MLSS was markedly less. Increased EPS adhesion to the membrane can accelerate TMP increase during the operation of both the AnMBR and the OCT filtration cell. EPS's reduced viscoelasticity at 25 °C suggests reduced floc integrity and possible increased EPS penetration into the membrane pores. Analysis of the structures of the microbial communities constituting the AnMBR flocs and membrane biofilms reveals temperature's effects on microbial richness, diversity, and abundance, which likely influence the observed EPS properties and consequent AnMBR fouling.

The welfare of farmed fish is influenced by numerous environmental and management factors. Fish skin is an important site for immunity and a major route by which infections are acquired. The objective of this study was to characterize bacterial composition variability on skin of healthy, diseased, and recovered Gilthead Seabream (Sparus aurata) and Barramundi (Lates calcarifer). S. aurata, which are highly sensitive to gram-negative bacteria, were challenged with Vibrio harveyi. In addition, and to provide a wider range of infections, both fish species (S. aurata and L. calcarifer) were infected with gram-positive Streptococcus iniae, to compare the response of the highly sensitive L. calcarifer to that of the more resistant S. aurata. All experiments also compared microbial communities found on skin of fish reared in UV (a general practice used in aquaculture) and non-UV treated water tanks. Skin swab samples were taken from different areas of the fish (lateral lines, abdomen and gills) prior to controlled infection, and 24, 48 and 72 h, 5 days, one week and one-month post-infection. Fish skin microbial communities were determined using Illumina iSeq100 16S rDNA for bacterial sequencing. The results showed that naturally present bacterial composition is similar on all sampled fish skin sites prior to infection, but the controlled infections (T1 24 h post infection) altered the bacterial communities found on fish skin. Moreover, when the naturally occurring skin microbiota did not quickly recover, fish mortality was common following T1 (24 h post infection). We further confirmed the differences in bacterial communities found on skin and in the water of fish reared in non-UV and UV treated water under healthy and diseased conditions. Our experimental findings shed light on the fish skin microbiota in relation to fish survival (in diseased and healthy conditions). The results can be harnessed to provide management tools for commercial fish farmers; predicting and preventing fish diseases can increase fish health, welfare, and enhance commercial fish yields.

Freshwater bodies are critical components of terrestrial ecosystems. The microbial communities of freshwater ecosystems are intimately linked water quality. These microbes interact with, utilize and recycle inorganic elements and organic matter. Here, we present three metagenomic sequence datasets (total of 182.9 Gbp) from different freshwater environments in Israel. The first dataset is from diverse freshwater bodies intended for different usages – a nature reserve, irrigation and aquaculture facilities, a tertiary wastewater treatment plant and a desert rainfall reservoir. The second represents a two-year time-series, collected during 2013–2014 at roughly monthly intervals, from a water reservoir connected to an aquaculture facility. The third is from several time-points during the winter and spring of 2015 in Lake Kinneret, including a bloom of the cyanobacterium Microcystis sp. These datasets are accompanied by physical, chemical, and biological measurements at each sampling point. We expect that these metagenomes will facilitate a wide range of comparative studies that seek to illuminate new aspects of freshwater microbial ecosystems and inform future water quality management approaches.

Antiscalants are organic polymers widely used for scale inhibition in seawater desalination. While they are susceptible to biodegradation, they provide nutrients for bacterial cell growth and energy for the microbes that assimilate and degrade them. This paper shows the biodegradability of three commercial antiscalants (polyacrylate—CA, polyphosphonate—PP, and carboxylated dendrimers—DN) applied in seawater reverse osmosis desalination (SWRO) as well as analyzing the antiscalant’s effects on microbial diversity using microbial cultures grown in seawater, under semi-continuous batch conditions. Nutritional uptake and contribution of the antiscalants to microbial growth were investigated by measuring DOC, TDN, NO₃⁻, NO₂⁻, PO₄⁻, NH₄⁺, and TP of the filtered samples of the incubated batch, twice a month, for twelve months. The microbial community was estimated by 16S rRNA sequencing. The main changes in the microbial communities were determined by the incubation period. However, bacterial orders of the antiscalant treatments differed significantly from the control treatment, namely Planctomycetales, Clostridiales, Sphingobacteriales, Rhodobacterales, and Flavobacteriales, and other unclassified bacterial orders, which were found in various relative abundances dependent on incubation times. The results showed the PP antiscalant to be the least biodegradable and to have the least effect on the bacterial community composition compared to the control. This result emphasizes the need to reassess the suitability criteria of antiscalants, and to further monitor their long-term environmental effects.

In the oceans and seas, environmental conditions change over multiple temporal and spatial scales. Here, we ask what factors affect the bacterial community structure across time, depth and size fraction during six seasonal cruises (2 years) in the ultra-oligotrophic Eastern Mediterranean Sea. The bacterial community varied most between size fractions (free-living (FL) vs. particle-associated), followed by depth and finally season. The FL community was taxonomically richer and more stable than the particle-associated (PA) one, which was characterized by recurrent ‘blooms’ of heterotrophic bacteria such as Alteromonas and Ralstonia. The heterotrophic FL and PA communities were also correlated with different environmental parameters: the FL population correlated with depth and phytoplankton, whereas PA bacteria were correlated primarily with the time of sampling. A significant part of the variability in community structure could, however, not be explained by the measured parameters. The metabolic potential of the PA community, predicted from 16S rRNA amplicon data using PICRUSt, was enriched in pathways associated with the degradation and utilization of biological macromolecules, as well as plastics, other petroleum products and herbicides. The FL community was enriched in predicted pathways for the metabolism of inositol phosphate, a potential phosphorus source, and of polycyclic aromatic hydrocarbons.

Background: The evolutionary relationships between plants and their microbiomes are of high importance to the survival of plants in general and even more in extreme conditions. Changes in the plant's microbiome can affect plant development, growth, fitness, and health. Along the arid Arava, southern Israel, acacia trees (Acacia raddiana and Acacia tortilis) are considered keystone species. In this study, we investigated the ecological effects of plant species, microclimate, phenology, and seasonality on the epiphytic and endophytic microbiome of acacia trees. One hundred thirty-nine leaf samples were collected throughout the sampling year and were assessed using 16S rDNA gene amplified with five different primers (targeting different gene regions) and sequenced (150 bp paired-end) on an Illumina MiSeq sequencing platform. Results: Epiphytic bacterial diversity indices (Shannon-Wiener, Chao1, Simpson, and observed number of operational taxonomic units) were found to be nearly double compared to endophyte counterparts. Epiphyte and endophyte communities were significantly different from each other in terms of the composition of the microbial associations. Interestingly, the epiphytic bacterial diversity was similar in the two acacia species, but the canopy sides and sample months exhibited different diversity, whereas the endophytic bacterial communities were different in the two acacia species but similar throughout the year. Abiotic factors, such as air temperature and precipitation, were shown to significantly affect both epiphyte and endophytes communities. Bacterial community compositions showed that Firmicutes dominate A. raddiana, and Proteobacteria dominate A. tortilis; these bacterial communities consisted of only a small number of bacterial families, mainly Bacillaceae and Comamonadaceae in the endophyte for A. raddiana and A. tortilis, respectively, and Geodematophilaceae and Micrococcaceae for epiphyte bacterial communities, respectively. Interestingly, ~60% of the obtained bacterial classifications were unclassified below family level (i.e., "new"). Conclusions: These results shed light on the unique desert phyllosphere microbiome highlighting the importance of multiple genotypic and abiotic factors in shaping the epiphytic and endophytic microbial communities. This study also shows that only a few bacterial families dominate both epiphyte and endophyte communities, highlighting the importance of climate change (precipitation, air temperature, and humidity) in affecting arid land ecosystems where acacia trees are considered keystone species.

Aquaculture facilities such as fishponds are one of the most anthropogenically impacted freshwater ecosystems. The high fish biomass reared in aquaculture is associated with an intensive input into the water of fish-feed and fish excrements. This nutrients load may affect the microbial community in the water, which in turn can impact the fish health. To determine to what extent aquaculture practices and natural seasonal cycles affect the microbial populations, we characterized the microbiome of an inter-connected aquaculture system at monthly resolution, over 3 years. The system comprised two fishponds, where fish are grown, and an operational water reservoir in which fish are not actively stocked. Clear natural seasonal cycles of temperature and inorganic nutrients concentration, as well as recurring cyanobacterial blooms during summer, were observed in both the fishponds and the reservoir. The structure of the aquatic bacterial communities in the system, characterized using 16S rRNA sequencing, was explained primarily by the natural seasonality, whereas aquaculture-related parameters had only a minor explanatory power. However, the cyanobacterial blooms were characterized by different cyanobacterial clades dominating at each fishpond, possibly in response to distinct nitrogen and phosphate ratios. In turn, nutrient ratios may have been affected by the magnitude of fish feed input. Taken together, our results show that, even in strongly anthropogenically impacted aquatic ecosystems, the structure of bacterial communities is mainly driven by the natural seasonality, with more subtle effects of aquaculture-related factors.

Excessive use of antimicrobials in aquaculture is concerning, given possible environmental ramifications and the potential contribution to the spread of antimicrobial resistance (AR). In this study, we explored seasonal abundance of antimicrobial resistance genes and bacterial community composition in the water column of an intensive aquaculture pond stocked with Silver Carp (Hypophthalmichthys molitrix) prophylactically treated with sulfamethoprim (25% sulfadiazine; 5% trimethoprim), relative to an adjacent unstocked reservoir. Bacterial community composition was monitored using high-throughput sequencing of 16S rRNA gene amplicons in eight sampling profiles to determine seasonal dynamics, representing principal stages in the fish fattening cycle. In tandem, qPCR was applied to assess relative abundance of selected antimicrobial resistance genes (sul1, sul2, dfrA1, tetA and blaTEM) and class-1 integrons (int1). Concomitantly, resistomes were extrapolated from shotgun metagenomes in representative profiles. Analyses revealed increased relative abundance of sulfonamide and tetracycline resistance genes in fishpond-03, relative to pre-stocking and reservoir levels, whereas no significant differences were observed for genes encoding resistance to antimicrobials that were not used in the fishpond-03. Seasons strongly dictated bacterial community composition, with high abundance of cyanobacteria in summer and increased relative abundance of Flavobacterium in the winter. Our results indicate that prophylactic use of sulfonamides in intensive aquaculture ponds facilitates resistance suggesting that prophylactic use of these antimicrobials in aquaculture should be restricted.

The effect of dietary omega-6 long-chain polyunsaturated fatty acid (LC-PUFA) on host microbiome and gut associated immune function in fish is unexplored. The effect of dietary supplementation with the omega-6 LC-PUFA-rich microalga Lobosphaera incisa wild type (WT) and its delta-5 desaturase mutant (MUT), rich in arachidonic-acid and dihomo-gamma-linolenic acid (DGLA), respectively, on intestinal gene expression and microbial diversity was analyzed in zebrafish. For 1 month, fish were fed diets supplemented with broken biomass at 7.5% and 15% (w/w) of the two L. incisa strains and a control nonsupplemented commercial diet. Dietary supplementation resulted in elevated expression of genes related to arachidonic acid metabolism-cyclooxygenase 2 (cox-2), lipoxygenase 1(lox-1), anti-inflammatory cytokine-interleukin 10 (il-10), immune defense-lysozyme (lys), intestinal alkaline phosphatase (iap), complement (c3b), and antioxidants-catalase (cat), glutathione peroxidase (gpx). Microbiome analysis of the gut showed higher diversity indices for microbial communities in fish that were fed the supplemented diets compared to controls. Different treatment groups shared 237 operational taxonomic units (OTUs) that corresponded to the core microbiome, and unique OTUs were evident in different dietary groups. Overall, the zebrafish gut microbiome was dominated by the phylum Fusobacteria and Proteobacteria (averaging 38.4% and 34.6%, respectively), followed by Bacteroidetes (12.9%), Tenericutes, Planctomycetes, and Actinobacteria (at 3.1–1.3%). Significant interaction between some of the immune-related genes and microbial community was demonstrated.

Lakes and other freshwater bodies are intimately connected to the surrounding land, yet to what extent land-use affects the quality of freshwater and the microbial communities living in various freshwater environments is largely unknown. We address this question through an analysis of the land use surrounding 46 inter-connected lakes located within seven different drainage basins in northern Germany, and the microbiomes of these lakes during early summer. Lake microbiome structure was not correlated with the specific drainage basin or by basin size, and bacterial distribution did not seem to be limited by distance. Instead, land use within the drainage basin could predict, to some extent, NO2 + NO3 concentrations in the water, which (together with temperature, chlorophyll a and total phosphorus) correlated to some extent with the water microbiome structure. Land use directly surrounding the water bodies, however, had little observable effects on water quality or the microbiome. Several microbial lineages, including Cyanobacteria and Verrucomicrobia, were differentially partitioned between the lakes. Significantly more data, including time-series measurements of land use and water chemical properties, are needed to fully understand the interaction between the environment and the organization of microbial communities.