Freshwater microbial metagenomes sampled across different water body characteristics, space and time in Israel.

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 Used in Seawater Desalination: Biodegradability and Effects on Microbial Diversity.

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.

Sparus aurata and Lates calcarifer skin microbiota under healthy and diseased conditions in UV and non-UV treated water.

BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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.

Temporal and Spatial Changes in Phyllosphere Microbiome of Acacia Trees Growing in Arid Environments.

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.

Seasonal Dynamics Are the Major Driver of Microbial Diversity and Composition in Intensive Freshwater Aquaculture.

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.

Particle-associated and free-living bacterial communities in an oligotrophic sea are affected by different environmental factors.

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.

Temporal Resistome and Microbial Community Dynamics in an Intensive Aquaculture Facility with Prophylactic Antimicrobial Treatment.

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.

Dietary Supplementation with Omega-6 LC-PUFA-Rich Microalgae Regulates Mucosal Immune Response and Promotes Microbial Diversity in the Zebrafish Gut.

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.

The Role of Land Use Types and Water Chemical Properties in Structuring the Microbiomes of a Connected Lake System.

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.

Temporal Stability of the Healthy Human Skin Microbiome Following Dead Sea Climatotherapy.

Dead Sea climatotherapy (DSC) is a therapeutic modality for a variety of chronic skin conditions, yet there has been scarce research on the relationship between the cutaneous microbiota and disease states in response to DSC. We characterized the skin bacterial and fungal microbiome of healthy volunteers who underwent DSC. Bacterial community diversity remained similar before and after treatment, while fungal diversity was significantly reduced as a result of the treatment. Individuals showed greater inter-individual than temporal bacterial community variance, yet the opposite was true for fungal community composition. We further identified Malassezia as the genus driving temporal mycobiome variations. The results indicate that the microbiome remains stable throughout DSC, while the mycobiome undergoes dramatic community changes. The results of this study will serve as an important baseline for future investigations of microbiome and mycobiome temporal phenomena in diseased states.

Biofouling of reverse osmosis membranes: effects of cleaning on biofilm microbial communities, membrane performance, and adherence of extracellular polymeric substances.

Laboratory-scale reverse osmosis (RO) flat-sheet systems were used with two parallel flow cells, one treated with cleaning agents and a control (ie undisturbed). The cleaning efforts increased the affinity of extracellular polymeric substances (EPS) to the RO membrane and altered the biofilm surface structure. Analysis of the membrane biofilm community composition revealed the dominance of Proteobacteria. However, within the phylum Proteobacteria, γ-Proteobacteria dominated the cleaned membrane biofilm, while ß-Proteobacteria dominated the control biofilm. The composition of the fungal phyla was also altered by cleaning, with enhancement of Ascomycota and suppression of Basidiomycota. The results suggest that repeated cleaning cycles select for microbial groups that strongly attach to the RO membrane surface by producing rigid and adhesive EPS that hampers membrane performance.

Biofouling of reverse-osmosis membranes under different shear rates during tertiary wastewater desalination: microbial community composition.

We investigated the influence of feed-water shear rate during reverse-osmosis (RO) desalination on biofouling with respect to microbial community composition developed on the membrane surface. The RO membrane biofilm's microbial community profile was elucidated during desalination of tertiary wastewater effluent in a flat-sheet lab-scale system operated under high (555.6 s(-1)), medium (370.4 s(-1)), or low (185.2 s(-1)) shear rates, corresponding to average velocities of 27.8, 18.5, and 9.3 cm s(-1), respectively. Bacterial diversity was highest when medium shear was applied (Shannon-Weaver diversity index H' = 4.30 ± 0.04) compared to RO-membrane biofilm developed under lower and higher shear rates (H' = 3.80 ± 0.26 and H' = 3.42 ± 0.38, respectively). At the medium shear rate, RO-membrane biofilms were dominated by Betaproteobacteria, whereas under lower and higher shear rates, the biofilms were dominated by Alpha- and Gamma- Proteobacteria, and the latter biofilms also contained Deltaproteobacteria. Bacterial abundance on the RO membrane was higher at low and medium shear rates compared to the high shear rate: 8.97 × 10(8) ± 1.03 × 10(3), 4.70 × 10(8) ± 1.70 × 10(3) and 5.72 × 10(6) ± 2.09 × 10(3) copy number per cm(2), respectively. Interestingly, at the high shear rate, the RO-membrane biofilm's bacterial community consisted mainly of populations known to excrete high amounts of extracellular polymeric substances. Our results suggest that the RO-membrane biofilm's community composition, structure and abundance differ in accordance with applied shear rate. These results shed new light on the biofouling phenomenon and are important for further development of antibiofouling strategies for RO membranes.

Biofouling of reverse-osmosis membranes during tertiary wastewater desalination: microbial community composition.

Reverse-osmosis (RO) desalination is frequently used for the production of high-quality water from tertiary treated wastewater (TTWW). However, the RO desalination process is often hampered by biofouling, including membrane conditioning, microbial adhesion, and biofilm growth. The vast majority of biofilm exploration concentrated on the role of bacteria in biofouling neglecting additional microbial contributors, i.e., fungi and archaea. To better understand the RO biofouling process, bacterial, archaeal and fungal diversity was characterized in a laboratory-scale RO desalination plant exploring the TTWW (RO feed), the RO membrane and the RO feed tube biofilms. We sequenced 77,400 fragments of the ribosome small subunit-encoding gene (16S and 18S rRNA) to identify the microbial community members in these matrices. Our results suggest that the bacterial, archaeal but not fungal community significantly differ from the RO membrane biofouling layer to the feedwater and tube biofilm (P < 0.01). Moreover, the RO membrane supported a more diverse community compared to the communities monitored in the feedwater and the biofilm attached to the RO feedwater tube. The tube biofilm was dominated by Actinobacteria (91.2 ± 4.6%), while the Proteobacteria phylum dominated the feedwater and RO membrane (at relative abundance of 92.3 ± 4.4% and 71.5 ± 8.3%, respectively), albeit comprising different members. The archaea communities were dominated by Crenarchaeota (53.0 ± 6.9%, 32.5 ± 7.2% and 69%, respectively) and Euryarchaeota (43.3 ± 6.3%, 23.2 ± 4.8% and 24%, respectively) in all three matrices, though the communities' composition differed. But the fungal communities composition was similar in all matrices, dominated by Ascomycota (97.6 ± 2.7%). Our results suggest that the RO membrane is a selective surface, supporting unique bacterial, and to a lesser extent archaeal communities, yet it does not select for a fungal community.

Spatial and temporal biogeography of soil microbial communities in arid and semiarid regions.

Microbial communities in soils may change in accordance with distance, season, climate, soil texture and other environmental parameters. Microbial diversity patterns have been extensively surveyed in temperate regions, but few such studies attempted to address them with respect to spatial and temporal scales and their correlations to environmental factors, especially in arid ecosystems. In order to fill this gap on a regional scale, the molecular fingerprints and abundance of three taxonomic groups--Bacteria, α-Proteobacteria and Actinobacteria--were sampled from soils 0.5-100 km apart in arid, semi-arid, dry Mediterranean and shoreline Mediterranean regions in Israel. Additionally, on a local scale, the molecular fingerprints of three taxonomic groups--Bacteria, Archaea and Fungi--were sampled from soils 1 cm-500 m apart in the semi-arid region, in both summer and winter. Fingerprints of the Bacteria differentiated between all regions (P<0.02), while those of the α-Proteobacteria differentiated between some of the regions (0.010.05). Locally, fingerprints of archaea and fungi did not display distance-decay relationships (P>0.13), that is, the dissimilarity between communities did not increase with geographic distance. Neither was this phenomenon evident in bacterial samples in summer (P>0.24); in winter, however, differences between bacterial communities significantly increased as the geographic distances between them grew (P<0.01). Microbial community structures, as well as microbial abundance, were both significantly correlated to precipitation and soil characteristics: texture, organic matter and water content (R(2)>0.60, P<0.01). We conclude that on the whole, microbial biogeography in arid and semi-arid soils in Israel is determined more by specific environmental factors than geographic distances and spatial distribution patterns.

Soil microbial abundance and diversity along a low precipitation gradient.

The exploration of spatial patterns of abundance and diversity patterns along precipitation gradients has focused for centuries on plants and animals; microbial profiles along such gradients are largely unknown. We studied the effects of soil pH, nutrient concentration, salinity, and water content on bacterial abundance and diversity in soils collected from Mediterranean, semi-arid, and arid sites receiving approximately 400, 300, and 100 mm annual precipitation, respectively. Bacterial diversity was evaluated by terminal restriction fragment length polymorphism and clone library analyses and the patterns obtained varied with the climatic regions. Over 75% of the sequenced clones were unique to their environment, while ∼2% were shared by all sites, yet, the Mediterranean and semi-arid sites had more common clones (∼9%) than either had with the arid site (4.7% and 6%, respectively). The microbial abundance, estimated by phospholipid fatty acids and real-time quantitative PCR assays, was significantly lower in the arid region. Our results indicate that although soil bacterial abundance decreases with precipitation, bacterial diversity is independent of precipitation gradient. Furthermore, community composition was found to be unique to each ecosystem.