Microbial metagenomics in the Baltic Sea: Recent advancements and prospects for environmental monitoring

Biodiversity of microorganisms in the Baltic Sea: the power of novel methods in the identification of marine microbes

Until recently, the data on the diversity of the entire microbial community from the Baltic Sea were relatively rare and very scarce. However, modern molecular methods have provided new insights into this field with interesting results. They can be summarized as follows. (i) Although low salinity causes a reduction in the biodiversity of multicellular species relative to the populations of the North-East Atlantic, no such reduction occurs in bacterial diversity. (ii) Among cyanobacteria, the picocyanobacterial group dominates when considering gene abundance, while filamentous cyanobacteria dominate in means of biomass. (iii) The diversity of diatoms and dinoflagellates is significantly larger than described a few decades ago; however, molecular studies on these groups are still scarce. (iv) Knowledge gaps in other protistan communities are evident. (v) Salinity is the main limiting parameter of pelagic fungal community composition, while the benthic fungal diversity is shaped by water depth, salinity, and sediment C and N availability. (vi) Bacteriophages are the predominant group of viruses, while among viruses infecting eukaryotic hosts, Phycodnaviridae are the most abundant; the Baltic Sea virome is contaminated with viruses originating from urban and/or industrial habitats. These features make the Baltic Sea microbiome specific and unique among other marine environments.

A metagenome-derived artificial intelligence modeling framework advances the predictive diagnosis and interpretation of petroleum-polluted groundwater

Groundwater (GW) quality monitoring is vital for sustainable water resource management. The present study introduced a metagenome-derived machine learning (ML) model aimed at enhancing the predictive understanding and diagnostic interpretation of GW pollution associated with petroleum. In this framework, taxonomic and metabolic profiles derived from GW metagenomes were combined for use as the input dataset. By employing strategies that optimized data integration, model selection, and parameter tuning, we achieved a significant increase in diagnostic accuracy for petroleum-polluted GW. Explanatory artificial intelligence techniques identified petroleum degradation pathways and Rhodocyclaceae as strong predictors of a pollution diagnosis. Metagenomic analysis corroborated the presence of gene operons encoding aminobenzoate and xylene biodegradation within the de novo assembled genome of Rhodocyclaceae. Our genome-centric metagenomic analysis thus clarified the ecological interactions associated with microbiomes in breaking down petroleum contaminants, validating the ML-based diagnostic results. This metagenome-derived ML framework not only enhances the predictive diagnosis of petroleum pollution but also offers interpretable insights into the interaction between microbiomes and petroleum. The proposed ML framework demonstrates great promise for use as a science-based strategy for the on-site monitoring and remediation of GW pollution.

Dynamics of nitrogen genes in intertidal sediments of Darwin Harbour and their connection to N-biogeochemistry

Microbial mediated nitrogen (N) transformation is subject to multiple controlling factors such as prevailing physical and chemical conditions, and little is known about these processes in sediments of wet-dry tropical macrotidal systems such as Darwin Harbour in North Australia. To understand key transformations, we assessed the association between the relative abundance of nitrogen cycling genes with trophic status, sediment partition and benthic nitrogen fluxes in Darwin Harbour. We analysed nitrogen cycling gene abundance using a functional gene microarray and quantitative PCRs targeting the denitrification gene (nosZ) and archaeal ammonia oxidation (AOA.1). We found a significant negative correlation between archaeal ammonia oxidation and silicate flux (P = 0.004), an indicator for diatom and benthic microalgal activity. It is suggested that the degradation of the diatomaceous organic matter generates localised anoxic conditions and inhibition of nitrification. Abundance of the nosZ gene was negatively correlated with nutrient load. The lowest nosZ gene levels were in hyper-eutrophic tidal creeks with anoxic conditions and increased levels of sulphide limiting the coupling of nitrification-denitrification (P = 0.016). Significantly higher levels of nosZ genes were measured in the surface (top 2 cm) compared to bulk sediment (top 10 cm) and there was a positive association with di-nitrogen flux (N2) in surface (P = 0.024) but not bulk sediment. This suggests that denitrifiers are most active in surficial sediment at the sediment-water interface. Elevated levels of nosZ genes also occurred in the sediments of tidal creek mouths and mudflats with these depositional zones combining the diffuse and seaward supply of nitrogen and carbon supporting denitrifiers. N-cycle molecular assays using surface sediments show promise as a rapid monitoring technique for impact assessment and measuring ecosystem function. This is particularly pertinent for tropical macrotidal systems where systematic monitoring is sparse and in many cases challenged by climatic extremes and remoteness.

Bacterial diversity in the aquatic system in India based on metagenome analysis-a critical review

Microbial analysis has become one of the most critical areas in aquatic ecology and a crucial component for assessing the contribution of microbes in food web dynamics and biogeochemical processes. Initial research was focused on estimating the abundance and distribution of the microbes using microscopy and culture-based analysis, which are undoubtedly complex tasks. Over the past few decades, microbiologists have endeavored to apply and extend molecular techniques to address pertinent questions related to the function and metabolism of microbes in aquatic ecology. Metagenomics analysis has revolutionized aquatic ecology studies involving the investigation of the genome of a mixed community of organisms in an ecosystem to identify microorganisms, their functionality, and the discovery of novel proteins. This review discusses the metagenomics analysis of bacterial diversity in and around different aquatic systems in India.

Unifying approaches to Functional Marine Connectivity for improved marine resource management: the European SEA-UNICORN COST Action

Truly sustainable development in a human-altered, fragmented marine environment subject to unprecedented climate change, demands informed planning strategies in order to be successful. Beyond a simple understanding of the distribution of marine species, data describing how variations in spatio-temporal dynamics impact ecosystem functioning and the evolution of species are required. Marine Functional Connectivity (MFC) characterizes the flows of matter, genes and energy produced by organism movements and migrations across the seascape. As such, MFC determines the ecological and evolutionary interdependency of populations, and ultimately the fate of species and ecosystems. Gathering effective MFC knowledge can therefore improve predictions of the impacts of environmental change and help to refine management and conservation strategies for the seas and oceans. Gathering these data are challenging however, as access to, and survey of marine ecosystems still presents significant challenge. Over 50 European institutions currently investigate aspects of MFC using complementary methods across multiple research fields, to understand the ecology and evolution of marine species. The aim of SEA-UNICORN, a COST Action supported by COST (European Cooperation in Science and Technology), is to bring together this research effort, unite the multiple approaches to MFC, and to integrate these under a common conceptual and analytical framework. The consortium brings together a diverse group of scientists to collate existing MFC data, to identify knowledge gaps, to enhance complementarity among disciplines, and to devise common approaches to MFC. SEA-UNICORN will promote co-working between connectivity practitioners and ecosystem modelers to facilitate the incorporation of MFC data into the predictive models used to identify marine conservation priorities. Ultimately, SEA-UNICORN will forge strong forward-working links between scientists, policy-makers and stakeholders to facilitate the integration of MFC knowledge into decision support tools for marine management and environmental policies.

Unifying approaches to Functional Marine Connectivity for improved marine resource management: the European SEA-UNICORN COST Action

Truly sustainable development in a human-altered, fragmented marine environment subject to unprecedented climate change, demands informed planning strategies in order to be successful. Beyond a simple understanding of the distribution of marine species, data describing how variations in spatio-temporal dynamics impact ecosystem functioning and the evolution of species are required. Marine Functional Connectivity (MFC) characterizes the flows of matter, genes and energy produced by organism movements and migrations across the seascape. As such, MFC determines the ecological and evolutionary interdependency of populations, and ultimately the fate of species and ecosystems. Gathering effective MFC knowledge can therefore improve predictions of the impacts of environmental change and help to refine management and conservation strategies for the seas and oceans. Gathering these data are challenging however, as access to, and survey of marine ecosystems still presents significant challenge. Over 50 European institutions currently investigate aspects of MFC using complementary methods across multiple research fields, to understand the ecology and evolution of marine species. The aim of SEA-UNICORN, a COST Action within the European Union Horizon 2020 framework programme, is to bring together this research effort, unite the multiple approaches to MFC, and to integrate these under a common conceptual and analytical framework. The consortium brings together a diverse group of scientists to collate existing MFC data, to identify knowledge gaps, to enhance complementarity among disciplines, and to devise common approaches to MFC. SEA-UNICORN will promote co-working between connectivity practitioners and ecosystem modelers to facilitate the incorporation of MFC data into the predictive models used to identify marine conservation priorities. Ultimately, SEA-UNICORN will forge strong forward-working links between scientists, policy-makers and stakeholders to facilitate the integration of MFC knowledge into decision support tools for marine management and environmental policies.

The Baltic Sea methane pockmark microbiome: The new insights into the patterns of relative abundance and ANME niche separation

Pockmarks are important "pumps", which are believed to play a significant role in the global methane cycling and harboring a unique assemblage of very diverse prokaryotes. This study reports the results of massive sequencing of the 16S rRNA gene V4 hypervariable regions for the samples from thirteen pockmark horizons (the Baltic Sea) collected at depths from 0 to 280 cm below seafloor (cmbsf) and the rates of microbially mediated anaerobic oxidation of methane (AOM) and sulfate reduction (SR). Altogether, 76 bacterial and 12 archaeal phyla were identified, 23 of which were candidate divisions. Of the total obtained in the pockmark sequences, 84.3% of them were classified as Bacteria and 12.4% as Archaea; 3.3% of the sequences were assigned to unknown operational taxonomic units (OTUs). Members of the phyla Planctomycetota, Chloroflexota, Desulfobacterota, Caldatribacteriota, Acidobacteriota and Proteobacteria predominated across all horizons, comprising 58.5% of the total prokaryotic community. These phyla showed different types of patterns of relative abundance. Analysis of AOM-SR-mediated prokaryotes abundance and biogeochemical measurements revealed that ANME-2a-2b subcluster was predominant in sulfate-rich upper horizons (including sulfate-methane transition zone (SMTZ)) and together with sulfate-reducing bacterial group SEEP-SRB1 had a primary role in AOM coupled to SR. At deeper sulfate-depleted horizons ANME-2a-2b shifted to ANME-1a and ANME-1b which alone mediated AOM or switch to methanogenic metabolism. Shifting of the ANME subclusters depending on depth reflect a tendency for niche separation in these groups. It was shown that the abundance of Caldatribacteriota and organohalide-respiring Dehalococcoidia (Chloroflexota) exhibited a strong correlation with AOM rates. This is the first detailed study of depth profiles of prokaryotic diversity, patterns of relative abundance, and ANME niche separation in the Baltic Sea pockmark microbiomes sheds light on assembly of prokaryotes in a pockmark.

Bacterial and eukaryotic microbial communities in urban water systems profiled via Illumina MiSeq platform

Microbial communities from a lake and river flowing through a highly dense urbanized township in Malaysia were profiled by sequencing amplicons of the 16S V3-V4 and 18S V9 hypervariable rRNA gene regions via Illumina MiSeq. Results revealed that Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes were the dominant prokaryotic phyla; whereas, eukaryotic communities were predominantly of the SAR clade and Opisthokonta. The abundance of Pseudomonas and Flavobacterium in all sites suggested the possible presence of pathogens in the urban water systems, supported by the most probable number (MPN) values of more than 1600 per 100 mL. Urbanization could have impacted the microbial communities as transient communities (clinical, water-borne and opportunistic pathogens) coexisted with common indigenous aquatic communities (Cyanobacteria). It was concluded that in urban water systems, microbial communities vary in their abundance of microbial phyla detected along the water systems. The influences of urban land use and anthropogenic activities influenced the physicochemical properties and the microbial dynamics in the water systems.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-020-02617-3.

How Copepods Can Eat Toxins Without Getting Sick: Gut Bacteria Help Zooplankton to Feed in Cyanobacteria Blooms

Toxin-producing cyanobacteria can be harmful to aquatic biota, although some grazers utilize them with often beneficial effects on their growth and reproduction. It is commonly assumed that gut microbiota facilitates host adaptation to the diet; however, the evidence for adaptation mechanisms is scarce. Here, we investigated the abundance of mlrA genes in the gut of the Baltic copepods Acartia bifilosa and Eurytemora affinis during cyanobacteria bloom season (August) and outside it (February). The mlrA genes are unique to microcystin and nodularin degraders, thus indicating the capacity to break down these toxins by the microbiota. The mlrA genes were expressed in the copepod gut year-round, being >10-fold higher in the summer than in the winter populations. Moreover, they were significantly more abundant in Eurytemora than Acartia. To understand the ecological implications of this variability, we conducted feeding experiments using summer- and winter-collected copepods to examine if/how the mlrA abundance in the microbiota affect: (1) uptake of toxic Nodularia spumigena, (2) uptake of a non-toxic algal food offered in mixtures with N. spumigena, and (3) concomitant growth potential in the copepods. The findings provide empirical evidence that the occurrence of mlrA genes in the copepod microbiome facilitates nutrient uptake and growth when feeding on phytoplankton mixtures containing nodularin-producing cyanobacteria; thus, providing an adaptation mechanism to the cyanobacteria blooms.

Metagenomics Uncovers a Core SAR11 Population in Brackish Surface Waters of the Baltic Sea

The Baltic Sea represents one of the largest brackish ecosystems where various environmental factors control dynamic seasonal shifts in the structure, diversity, and function of the planktonic microbial communities. In this study, despite seasonal fluctuations, several bacterial populations (<2% of the total OTUs) that are highly dominant (25% of relative abundance) and highly frequently occurring (>85% of occurrence) over four seasons were identified. Mathematical models using occurrence frequency and relative abundance data were able to describe community assembly persisting over time. Further, this work uncovered one of the core bacterial populations phylogenetically affiliated to SAR11 subclade IIIa. The analysis of the hypervariable region of 16S rRNA gene and single copy housekeeping genes recovered from metagenomic datasets suggested that the population was unexpectedly evolutionarily closely related to those inhabiting a mesosaline lacustrine ecosystem rather than other marine/coastal members. Our metagenomic results further revealed that the newly-identified population was the major driver facilitating the seasonal shifts in the overall community structure over the brackish waters of the Baltic Sea. The core community uncovered in this study supports the presence of a brackish water microbiome distinguishable from other marine and freshwater counterparts and will be a useful sentinel for monitoring local/global environmental changes posed on brackish surface waters.

Metabarcoding successfully tracks temporal changes in eukaryotic communities in coastal sediments

Metabarcoding is a method that combines high-throughput DNA sequencing and DNA-based identification. Previously, this method has been successfully used to target spatial variation of eukaryote communities in marine sediments, however, the temporal changes in these communities remain understudied. Here, we follow the temporal changes of the eukaryote communities in Baltic Sea surface sediments collected from two coastal localities during three seasons of two consecutive years. Our study reveals that the structure of the sediment eukaryotic ecosystem was primarily driven by annual and seasonal changes in prevailing environmental conditions, whereas spatial variation was a less significant factor in explaining the variance in eukaryotic communities over time. Therefore, our data suggests that shifts in regional climate regime or large-scale changes in the environment are the overdriving factors in shaping the coastal eukaryotic sediment ecosystems rather than small-scale changes in local environmental conditions or heterogeneity in ecosystem structure. More studies targeting temporal changes are needed to further understand the long-term trends in ecosystem stability and response to climate change. Furthermore, this work contributes to the recent efforts in developing metabarcoding applications for environmental biomonitoring, proving a comprehensive option for traditional monitoring approaches.

Microbiota fingerprints within the oral cavity of cetaceans as indicators for population biomonitoring

The composition of mammalian microbiota has been related with the host health status. In this study, we assessed the oral microbiome of 3 cetacean species most commonly found stranded in Iberian Atlantic waters (Delphinus delphis, Stenella coeruleoalba and Phocoena phocoena), using 16S rDNA-amplicon metabarcoding. All oral microbiomes were dominated by Proteobacteria, Firmicutes, Bacteroidetes and Fusobacteria bacteria, which were also predominant in the oral cavity of Tursiops truncatus. A Constrained Canonical Analysis (CCA) showed that the major factors shaping the composition of 38 oral microbiomes (p-value < 0.05) were: (i) animal species and (ii) age class, segregating adults and juveniles. The correlation analysis also grouped the microbiomes by animal stranding location and health status. Similar discriminatory patterns were detected using the data from a previous study on Tursiops truncatus, indicating that this correlation approach may facilitate data comparisons between different studies on several cetacean species. This study identified a total of 15 bacterial genera and 27 OTUs discriminating between the observed CCA groups, which can be further explored as microbiota fingerprints to develop (i) specific diagnostic assays for cetacean population conservation and (ii) bio-monitoring approaches to assess the health of marine ecosystems from the Iberian Atlantic basin, using cetaceans as bioindicators.

Interactive effects of multiple stressors revealed by sequencing total (DNA) and active (RNA) components of experimental sediment microbial communities

Coastal waterways are increasingly exposed to multiple stressors, e.g. contaminants that can be delivered via pulse or press exposures. Therefore, it is crucial that ecological impacts can be differentiated among stressors to manage ecosystem threats. We investigated microbial community development in sediments exposed to press and pulse stressors. Press exposures were created with in situ mesocosm sediments containing a range of 'metal' concentrations (sediment contaminated with multiple metal(loid)s) and organic enrichment (fertiliser), while the pulse exposure was simulated by a single dose of organic fertiliser. All treatments and exposure concentrations were crossed in a fully factorial field experiment. We used amplicon sequencing to compare the sensitivity of the 1) total (DNA) and active (RNA) component of 2) bacterial (16S rRNA) and eukaryotic (18S rRNA) communities to contaminant exposures. Overall microbial community change was greater when exposed to press than pulse stressors, with the bacterial community responding more strongly than the eukaryotes. The total bacterial community represents a more time-integrated measure of change and proved to be more sensitive to multiple stressors than the active community. Metals and organic enrichment treatments interacted such that the effect of metals was weaker when the sediment was organically enriched. Taxa-level analyses revealed that press enrichment resulted in potential functional changes, mainly involving nitrogen cycling. Furthermore, enrichment generally reduced the abundance of active eukaryotes in the sediment. As well as demonstrating interactive impacts of metals and organic enrichment, this study highlights the sensitivity of next-generation sequencing for ecosystem biomonitoring of interacting stressors and identifies opportunities for more targeted application.

Biodiversity of cyanobacteria and other aquatic microorganisms across a freshwater to brackish water gradient determined by shotgun metagenomic sequencing analysis in the San Francisco Estuary, USA

Blooms of Microcystis and other harmful cyanobacteria can degrade water quality by producing cyanotoxins or other toxic compounds. The goals of this study were (1) to facilitate understanding of community structure for various aquatic microorganisms in brackish water and freshwater regions with emphasis on cyanobacteria, and (2) to test a hypothesis that Microcystis genotypes that tolerate higher salinity were blooming in brackish water environments during the severe drought, 2014. Shotgun metagenomic analysis revealed that cyanobacteria dominated the brackish water region while bacteria dominated the freshwater region. A group of cyanobacteria (e.g., Aphanizomenon, Microcystis, Planktothrix, Pseudanabaena), bacteria (e.g., Bacillus, Porphyrobacter), and diatoms (Phaeodactylum and Thalassiosira) were abundant in the brackish water region. In contrast, Hassallia (cyanobacteria) and green algae (Nannochloropsis, Chlamydomonas, and Volvox) were abundant in the landward freshwater region. Station variation was also apparent. One landward sampling station located downstream of an urbanized area differed substantially from the other stations in terms of both water chemistry and community structure, with a higher percentage of arthropods, green algae, and eukaryotes. Screening of the Microcystis internal transcribed spacer region revealed six representative genotypes, and two of which were successfully quantified using qPCR (Genotypes I and VI). Both genotypes occurred predominantly in the freshwater region, so the data from this study did not support the hypothesis that salinity tolerant Microcystis genotypes bloomed in the brackish water region in 2014.

'Omic' technologies as a helpful tool in radioecological research

This article presents a brief review of the modern 'omic' technologies, namely genomics, epigenomics, transcriptomics, proteomics, and metabolomics, as well as the examples of their possible use in radioecology. For each technology, a short description of advances, limitations, and instrumental applications is given. In addition, the review contains examples of successful use of 'omic' technologies in the assessment of biological effects of pollutants in the field conditions.

Metagenomic Analysis of Cyanobacteria in an Oligotrophic Tropical Estuary, South Atlantic

This study assessed the species composition, distribution, and functional profiles of cyanobacteria in Camamu Bay, a tropical oligotrophic estuarine system on the northeast coast of Brazil, using shotgun metagenomic sequencing. Surface-water samples were evaluated in two different rainfall periods (rainy and dry seasons), at nine stations in the three hydrodynamic regions of the bay. At a fixed sampling station, on each season, samples were taken over a tidal cycle at 3-h intervals over 12 h. A total of 219 cyanobacterial taxa were identified, demonstrating a diverse community of freshwater, euryhaline, and marine cyanobacteria. The genera of greater relative abundance, Synechococcus and Prochlorococcus, corresponded to the picoplankton fraction. Although Camamu Bay has conspicuous marine characteristics, the contribution of freshwater during the rainy season caused variation in cyanobacteria community, with an increase in species richness. Due the high prevalence of Synechococcus (90% of the sequences), the functional analysis revealed only minor differences in gene content between the dry and rainy seasons. In both rainy and dry seasons, an increase in Prochlorococcus relative abundance occurred during high tide, demonstrating the tidal influence in the bay. The environmental characteristics of the bay provide niche conditions for a wide variety of cyanobacteria, including freshwater, euryhaline, and marine strains.

Vibrio Ecology in the Neuse River Estuary, North Carolina, Characterized by Next-Generation Amplicon Sequencing of the Gene Encoding Heat Shock Protein 60 (hsp60)

Of marine eubacteria, the genus Vibrio is intriguing because member species are relevant to both marine ecology and human health. Many studies have touted the relationships of Vibrio to environmental factors, especially temperature and salinity, to predict total Vibrio abundance but lacked the taxonomic resolution to identify the relationships among species and the key drivers of Vibrio dynamics. To improve next-generation sequencing (NGS) surveys of Vibrio, we have conducted both 16S small subunit rRNA and heat shock protein 60 (hsp60) amplicon sequencing of water samples collected at two well-studied locations in the Neuse River Estuary, NC. Samples were collected between May and December 2016 with enhanced sampling efforts in response to two named storms. Using hsp60 sequences, 21 Vibrio species were identified, including the potential human pathogens V. cholerae, V. parahaemolyticus, and V. vulnificus Changes in the Vibrio community mirrored seasonal and storm-related changes in the water column, especially in response to an influx of nutrient-rich freshwater to the estuary after Hurricane Matthew, which initiated dramatic changes in the overall Vibrio community. Individual species dynamics were wide ranging, indicating that individual Vibrio taxa have unique ecologies and that total Vibrio abundance predictors are insufficient for risk assessments of potentially pathogenic species. Positive relationships between Vibrio, dinoflagellates, and Cyanobacteria were identified, as were intraspecies associations, which further illuminated the interactions of cooccurring Vibrio taxa along environmental gradients.IMPORTANCE The objectives of this research were to utilize a novel approach to improve sequence-based surveys of Vibrio communities and to demonstrate the usefulness of this approach by presenting an analysis of Vibrio dynamics in the context of environmental conditions, with a particular focus on species that cause disease in humans and on storm effects. The methods presented here enabled the analysis of Vibrio dynamics with excellent taxonomic resolution and could be incorporated into future ecological studies and risk prediction strategies for potentially pathogenic species. Next-generation sequencing of hsp60 and other innovative sequence-based approaches are valuable tools and show great promise for studying Vibrio ecology and associated public health risks.

Analysis of bacterial metagenomes from the Southwestern Gulf of Mexico for pathogens detection

Little is known about the diversity of bacteria in the Southwestern Gulf of Mexico. The aim of the study illustrated in this perspective was to search for the presence of bacterial pathogens in this ecosystem, using metagenomic data recently generated by the Mexican research group known as the Gulf of Mexico Research Consortium. Several genera of bacteria annotated as pathogens were detected in water and sediment marine samples. As expected, native and ubiquitous pathogenic bacteria genera such as Burkolderia, Halomonas, Pseudomonas, Shewanella and Vibrio were highly represented. Surprisingly, non-native genera of public health concern were also detected, including Borrelia, Ehrlichia, Leptospira, Mycobacterium, Mycoplasma, Salmonella, Staphylococcus, Streptococcus and Treponema. While there are no previous metagenomics studies of this environment, the potential influences of natural, anthropogenic and ecological factors on the diversity of putative pathogenic bacteria found in it are reviewed. The taxonomic annotation herein reported provides a starting point for an improved understanding of bacterial biodiversity in the Southwestern Gulf of Mexico. It also represents a useful tool in public health as it may help identify infectious diseases associated with exposure to marine water and ingestion of fish or shellfish, and thus may be useful in predicting and preventing waterborne disease outbreaks.

Bacterial community diversity on in-shell walnut surfaces from six representative provinces in China

Walnuts (Juglans regia) have been associated with foodborne illness outbreaks in recent years. Thus, the purpose of this study was to investigate the distribution of bacteria on in-shell walnut surfaces from six representative provinces in China. The bacterial populations on walnut surfaces were investigated by high-throughput sequencing based on the bacterial 16 S rRNA hypervariable region V4. Twenty-eight samples were collected from fourteen regions in six provinces and harvested in different periods (the fresh in 2016 and the old in 2015). Proteobacteria was the most dominant phylum in all samples except for XJ1. In XJ1, and the most abundant phylum was Cyanobacteria, which also accounted for a large proportion of the abundance in YN1, YN11, XJ2 and SC11. In addition, Firmicutes and Actinobacteria were also the abundant phyla in the given samples. Some genera belonging to the opportunistic pathogens were detected, such as Pseudomonas, Acinetobacter, Burkholderia and Bacillus. The results revealed that the composition and abundance of bacterial consortiums on walnut surfaces varied among the geographical sites where they were harvested. Moreover, the storage time of samples also had impact on the abundance of bacteria. This study may provide a better understanding of the bacterial communities' diversity on in-shell walnut surfaces.

Evaluation of 16S rRNA Gene Primer Pairs for Monitoring Microbial Community Structures Showed High Reproducibility within and Low Comparability between Datasets Generated with Multiple Archaeal and Bacterial Primer Pairs

The application of next-generation sequencing technology in microbial community analysis increased our knowledge and understanding of the complexity and diversity of a variety of ecosystems. In contrast to Bacteria, the archaeal domain was often not particularly addressed in the analysis of microbial communities. Consequently, established primers specifically amplifying the archaeal 16S ribosomal gene region are scarce compared to the variety of primers targeting bacterial sequences. In this study, we aimed to validate archaeal primers suitable for high throughput next generation sequencing. Three archaeal 16S primer pairs as well as two bacterial and one general microbial 16S primer pairs were comprehensively tested by in-silico evaluation and performing an experimental analysis of a complex microbial community of a biogas reactor. The results obtained clearly demonstrate that comparability of community profiles established using different primer pairs is difficult. 16S rRNA gene data derived from a shotgun metagenome of the same reactor sample added an additional perspective on the community structure. Furthermore, in-silico evaluation of primers, especially those for amplification of archaeal 16S rRNA gene regions, does not necessarily reflect the results obtained in experimental approaches. In the latter, archaeal primer pair ArchV34 showed the highest similarity to the archaeal community structure compared to observed by the metagenomic approach and thus appears to be the appropriate for analyzing archaeal communities in biogas reactors. However, a disadvantage of this primer pair was its low specificity for the archaeal domain in the experimental application leading to high amounts of bacterial sequences within the dataset. Overall our results indicate a rather limited comparability between community structures investigated and determined using different primer pairs as well as between metagenome and 16S rRNA gene amplicon based community structure analysis. This finding, previously shown for Bacteria, was as well observed for the archaeal domain.

Monitoring and managing microbes in aquaculture - Towards a sustainable industry

Microorganisms are of great importance to aquaculture where they occur naturally, and can be added artificially, fulfilling different roles. They recycle nutrients, degrade organic matter and, occasionally, they infect and kill the fish, their larvae or the live feed. Also, some microorganisms may protect fish and larvae against disease. Hence, monitoring and manipulating the microbial communities in aquaculture environments hold great potential; both in terms of assessing and improving water quality, but also in terms of controlling the development of microbial infections. Using microbial communities to monitor water quality and to efficiently carry out ecosystem services within the aquaculture systems may only be a few years away. Initially, however, we need to thoroughly understand the microbiomes of both healthy and diseased aquaculture systems, and we need to determine how to successfully manipulate and engineer these microbiomes. Similarly, we can reduce the need to apply antibiotics in aquaculture through manipulation of the microbiome, i.e. by the use of probiotic bacteria. Recent studies have demonstrated that fish pathogenic bacteria in live feed can be controlled by probiotics and that mortality of infected fish larvae can be reduced significantly by probiotic bacteria. However, the successful management of the aquaculture microbiota is currently hampered by our lack of knowledge of relevant microbial interactions and the overall ecology of these systems.

Genome Reconstruction from Metagenomic Data Sets Reveals Novel Microbes in the Brackish Waters of the Caspian Sea

We present here the findings from a study of the microbiome of the southern basin of the Caspian Sea, the largest water body on Earth disconnected from any ocean and a brackish inland sea. By high-throughput metagenomics, we were able to reconstruct the genomes of representative microbes. The gross community structure (at the phylum level) was different from the structure of typical marine and freshwater communities in temperate open oceans, with the Caspian Sea having freshwater-like amounts of Actinobacteria and Alphaproteobacteria, while Gammaproteobacteria and Betaproteobacteria were present at intermediate levels. We assembled the genomes of several groups and provide detailed descriptions of partial genomes from Actinobacteria, Thaumarchaea, and Alphaproteobacteria. Most belonged to hitherto unknown groups, although they were related to either marine or freshwater groups. The phylogenetic placement of the Caspian genomes indicates that the organisms have multiple and separate phylogenetic origins and that they are related to organisms with both freshwater and marine lineages. Comparative recruitment from global aquatic metagenomes indicated that most Caspian microbes are endemic. However, some Caspian genomes were recruited significantly from either marine water (a member of the Alphaproteobacteria) or freshwater (a member of the Actinobacteria). Reciprocally, some genomes of other origins, such as the marine thaumarchaeon " Candidatus Nitrosopelagicus" or the actinobacterium "Candidatus Actinomarina," were recruited from the Caspian Sea, indicating some degree of overlap with the microbiota of other water bodies. Some of these microbes seem to have a remarkably widespread geographic and environmental distribution.

Baltic Sea ecosystem-based management under climate change: Synthesis and future challenges

Ecosystem-based management (EBM) has emerged as the generally agreed strategy for managing ecosystems, with humans as integral parts of the managed system. Human activities have substantial effects on marine ecosystems, through overfishing, eutrophication, toxic pollution, habitat destruction, and climate change. It is important to advance the scientific knowledge of the cumulative, integrative, and interacting effects of these diverse activities, to support effective implementation of EBM. Based on contributions to this special issue of AMBIO, we synthesize the scientific findings into four components: pollution and legal frameworks, ecosystem processes, scale-dependent effects, and innovative tools and methods. We conclude with challenges for the future, and identify the next steps needed for successful implementation of EBM in general and specifically for the Baltic Sea.