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Methane (CH4) from aquatic ecosystems contributes to about half of total global CH4 emissions to the atmosphere. Until recently, aquatic biogenic CH4 production was exclusively attributed to methanogenic archaea living under anoxic or suboxic conditions in sediments, bottom waters, and wetlands. However, evidence for oxic CH4 production (OMP) in freshwater, brackish, and marine habitats is increasing. Possible sources were found to be driven by various planktonic organisms supporting different OMP mechanisms. Surprisingly, submerged macrophytes have been fully ignored in studies on OMP, yet they are key components of littoral zones of ponds, lakes, and coastal systems. High CH4 concentrations in these zones have been attributed to organic substrate production promoting classic methanogenesis in the absence of oxygen. Here, we review existing studies and argue that, similar to terrestrial plants and phytoplankton, macroalgae and submerged macrophytes may directly or indirectly contribute to CH4 formation in oxic waters. We propose several potential direct and indirect mechanisms: (1) direct production of CH4; (2) production of CH4 precursors and facilitation of their bacterial breakdown or chemical conversion; (3) facilitation of classic methanogenesis; and (4) facilitation of CH4 ebullition. As submerged macrophytes occur in many freshwater and marine habitats, they are important in global carbon budgets and can strongly vary in their abundance due to seasonal and boom‐bust dynamics. Knowledge on their contribution to OMP is therefore essential to gain a better understanding of spatial and temporal dynamics of CH4 emissions and thus to substantially reduce current uncertainties when estimating global CH4 emissions from aquatic ecosystems. [ABSTRACT FROM AUTHOR]

Microbial communities are essential components of aquatic ecosystems through their contribution to food web dynamics and biogeochemical processes. Aquatic microbial diversity is immense and a general challenge is to understand how metabolism and interactions of single organisms shape microbial community dynamics and ecosystem‐scale biogeochemical transformations. Metagenomic approaches have developed rapidly, and proven to be powerful in linking microbial community dynamics to biogeochemical processes. In this review, we provide an overview of metagenomic approaches, followed by a discussion on some recent insights they have provided, including those in this special issue. These include the discovery of new taxa and metabolisms in aquatic microbiomes, insights into community assembly and functional ecology as well as evolutionary processes shaping microbial genomes and microbiomes, and the influence of human activities on aquatic microbiomes. Given that metagenomics can now be considered a mature technology where data generation and descriptive analyses are relatively routine and informative, we then discuss metagenomic‐enabled research avenues to further link microbial dynamics to biogeochemical processes. These include the integration of metagenomics into well‐designed ecological experiments, the use of metagenomics to inform and validate metabolic and biogeochemical models, and the pressing need for ecologically relevant model organisms and simple microbial systems to better interpret the taxonomic and functional information integrated in metagenomes. These research avenues will contribute to a more mechanistic and predictive understanding of links between microbial dynamics and biogeochemical cycles. Owing to rapid climate change and human impacts on aquatic ecosystems, the urgency of such an understanding has never been greater. [ABSTRACT FROM AUTHOR]

Mixotrophy is increasingly recognized as an important trophic pathway among phytoplankton, yet its underlying drivers remain largely unknown and unexplored. Here, we present a study utilizing 69 lake samplings in boreal Quebec, Canada, identifying variables driving the success of phytoplankton that have a capacity for mixotrophy and pointing to the underlying mechanisms. We found that the success of mixotrophs (% of total biomass) was positively influenced by both colored dissolved organic matter (cDOM) and dissolved CO2 concentration but limited by the abundance of crustacean zooplankton. The effect of cDOM manifested as a consequence of limited autotrophic phytoplankton biomass in lakes with reduced light penetration. We observed a nonlinear (u‐shaped) relation between CO2 and mixotrophs, with biomass favored at both low and high CO2 concentrations. A reduced fitness of mixotrophs at near‐atmospheric CO2 concentrations is likely owing to the costs of rapidly switching between or maintaining multiple trophic strategies. The abundance of zooplankton had a negative effect on mixotroph biomass but a positive effect on autotrophic phytoplankton. We also found that while the community composition of potentially mixotrophic phytoplankton was to some degree likely influenced by zooplankton biomass, composition was unaffected by the CO2 and cDOM gradients. Overall, this study highlights mixotrophy in boreal lake systems as a strategy of persistence, with the maintenance of a moderate but constant presence across a changing gradient of light and trophic conditions. The results of our study support the hypothesis that phytoplankton with a capacity for mixotrophy provide a superior and stable stoichiometric food source for zooplankton, implicating mixotrophs as a vital component of boreal lake food webs. [ABSTRACT FROM AUTHOR]

Growing attention to phytoplankton mixotrophy as a trophic strategy has led to significant revisions of traditional pelagic food web models and ecosystem functioning. Although some empirical estimates of mixotrophy do exist, a much broader set of in situ measurements are required to (i) identify which organisms are acting as mixotrophs in real time and to (ii) assess the contribution of their heterotrophy to biogeochemical cycling. Estimates are needed through time and across space to evaluate which environmental conditions or habitats favour mixotrophy: conditions still largely unknown. We review methodologies currently available to plankton ecologists to undertake estimates of plankton mixotrophy, in particular nanophytoplankton phago-mixotrophy. Methods are based largely on fluorescent or isotopic tracers, but also take advantage of genomics to identify phylotypes and function. We also suggest novel methods on the cusp of use for phago-mixotrophy assessment, including single-cell measurements improving our capacity to estimate mixotrophic activity and rates in wild plankton communities down to the single-cell level. Future methods will benefit from advances in nanotechnology, micromanipulation and microscopy combined with stable isotope and genomic methodologies. Improved estimates of mixotrophy will enable more reliable models to predict changes in food web structure and biogeochemical flows in a rapidly changing world. [ABSTRACT FROM AUTHOR]

Summary: Within the wealth of molecules constituting marine dissolved organic matter, carbohydrates make up the largest coherent and quantifiable fraction. Their main sources are from primary producers, which release large amounts of photosynthetic products – mainly polysaccharides – directly into the surrounding water via passive and active exudation. The organic carbon and other nutrients derived from these photosynthates enrich the ‘phycosphere’ and attract heterotrophic bacteria. The rapid uptake and remineralization of dissolved free monosaccharides by heterotrophic bacteria account for the barely detectable levels of these compounds. By contrast, dissolved combined polysaccharides can reach high concentrations, especially during phytoplankton blooms. Polysaccharides are too large to be taken up directly by heterotrophic bacteria, instead requiring hydrolytic cleavage to smaller oligo‐ or monomers by bacteria with a suitable set of exoenzymes. The release of diverse polysaccharides by various phytoplankton taxa is generally interpreted as the deposition of excess organic material. However, these molecules likely also fulfil distinct, yet not fully understood functions, as inferred from their active modulation in terms of quality and quantity when phytoplankton becomes nutrient limited or is exposed to heterotrophic bacteria. This minireview summarizes current knowledge regarding the exudation and composition of phytoplankton‐derived exopolysaccharides and acquisition of these compounds by heterotrophic bacteria. [ABSTRACT FROM AUTHOR]

Kettle holes are small inland waters formed from glacially-created depressions often situated in agricultural landscapes. Due to their high perimeter-to-area ratio facilitating a high aquatic-terrestrial coupling, kettle holes can accumulate high concentrations of organic carbon and nutrients, fueling microbial activities and turnover rates. Thus, they represent hotspots of carbon turnover in the landscape, but their bacterial activities and controlling factors have not been well investigated. Therefore, we aimed to assess the relative importance of various environmental factors on bacterial and biogeochemical processes in the water column of kettle holes and to disentangle their variations. In the water body of ten kettle holes in north-eastern Germany, we measured several physico-chemical and biological parameters such as carbon quantity and quality, as well as bacterial protein production (BP) and community respiration (CR) in spring, early summer and autumn 2014. Particulate organic matter served as an indicator of autochthonous production and represented an important parameter to explain variations in BP and CR. This notion is supported by qualitative absorbance indices of dissolved molecules in water samples and C:N ratios of the sediments, which demonstrate high fractions of autochthonous organic matter (OM) in the studied kettle holes. In contrast, dissolved chemical parameters were less important for bacterial activities although they revealed strong differences throughout the growing season. Pelagic bacterial activities and dynamics might thus be regulated by autochthonous OM in kettle holes implying a control of important biogeochemical processes by internal primary production rather than facilitated exchange with the terrestrial surrounding due to a high perimeter-to-area ratio. [ABSTRACT FROM AUTHOR]

Kettle holes as a specific group of isolated, small lentic freshwater systems (LFS) often are (i) hot spots of biogeochemical cycling and (ii) exposed to frequent sediment desiccation and rewetting. Their ecological functioning is greatly determined by immanent carbon and nutrient transformations. The objective of this review is to elucidate effects of a changing hydrological regime (i.e., dry-wet cycles) on carbon and nutrient cycling in kettle hole sediments. Generally, dry-wet cycles have the potential to increase C and N losses as well as P availability. However, their duration and frequency are important controlling factors regarding direction and intensity of biogeochemical and microbiological responses. To evaluate drought impacts on sediment carbon and nutrient cycling in detail requires the context of the LFS hydrological history. For example, frequent drought events induce physiological adaptation of exposed microbial communities and thus flatten metabolic responses, whereas rare events provoke unbalanced, strong microbial responses. Different potential of microbial resilience to drought stress can irretrievably change microbial communities and functional guilds, gearing cascades of functional responses. Hence, dry-wet events can shift the biogeochemical cycling of organic matter and nutrients to a new equilibrium, thus affecting the dynamic balance between carbon burial and mineralization in kettle holes. [ABSTRACT FROM AUTHOR]

Fungi constitute important and conspicuous components of aquatic microbial communities, but their diversity and functional roles remain poorly characterized. New methods and conceptual frameworks are required to accurately describe their ecological roles, involvement in global cycling processes, and utility for human activities, considering both cultivation-independent techniques as well as experiments in laboratory and in natural ecosystems. Here we highlight recent developments and extant knowledge gaps in aquatic mycology, and provide a conceptual model to expose the importance of fungi in aquatic food webs and related biogeochemical processes. [ABSTRACT FROM AUTHOR]

Copepods are exposed to a high non-predatory mortality and their decomposing carcasses act as microniches with intensified microbial activity. Sinking carcasses could thereby represent anoxic microenvironment sustaining anaerobic microbial pathways in otherwise oxic water columns. Using non-invasive O2 imaging, we document that carcasses of Calanus finmarchicus had an anoxic interior even at fully air-saturated ambient O2 level. The extent of anoxia gradually expanded with decreasing ambient O2 levels. Concurrent microbial sampling showed the expression of nitrite reductase genes ( nirS) in all investigated carcass samples and thereby documented the potential for microbial denitrification in carcasses. The nirS gene was occasionally expressed in live copepods, but not as consistently as in carcasses. Incubations of sinking carcasses in 15 [ABSTRACT FROM AUTHOR]

Phytoplankton-bacterium interactions are mediated, in part, by phytoplankton- released dissolved organic matter (DOMp). Two factors that shape the bacterial community accompanying phytoplankton are (i) the phytoplankton producer species, defining the initial composition of released DOMp, and (ii) the DOMp transformation over time. We added phytoplankton DOMp from the diatom Skeletonema marinoi and the cyanobacterium Prochlorococcus marinus MIT9312 to natural bacterial communities from the eastern Mediterranean and determined the bacterial responses over a time course of 72 h in terms of cell numbers, bacterial production, alkaline phosphatase activity, and changes in active bacterial community composition based on rRNA amplicon sequencing. Both DOMp types were demonstrated to serve the bacterial community as carbon and, potentially, phosphorus sources. Bacterial communities in diatom-derived DOM treatments maintained higher Shannon diversities throughout the experiment and yielded higher bacterial production and lower alkaline phosphatase activity compared to cyanobacterium-derived DOM after 24 h of incubation (but not after 48 and 72 h), indicating greater bacterial usability of diatom-derived DOM. Bacterial communities significantly differed between DOMp types as well as between different incubation times, pointing to a certain bacterial specificity for the DOMp producer as well as a successive utilization of phytoplankton DOM by different bacterial taxa over time. The highest differences in bacterial community composition with DOMp types occurred shortly after DOMp additions, suggesting a high specificity toward highly bioavailable DOMp compounds. We conclude that phytoplankton-associated bacterial communities are strongly shaped by the phyto-plankton producer as well as the transformation of its released DOMp over time. [ABSTRACT FROM AUTHOR]

In aquatic environments, community dynamics of bacteria, especially actively growing bacteria (AGB), are tightly linked with dissolved organic matter (DOM) quantity and quality. We analyzed the community dynamics of DNA-synthesizing and accordingly AGB by linking an improved bromodeoxyuridine immunocytochemistry approach with fluorescence-activated cell sorting (BrdU-FACS). FACS-sorted cells of even oligotrophic ecosystems in winter were characterized by 16S rRNA gene analysis. In incubation experiments, we examined community shifts of AGB in response to the addition of N-acetyl-glucosamine (NAG), one of the most abundant aminosugars in aquatic systems. Our improved BrdU-FACS analysis revealed that AGB winter communities of oligotrophic Lake Stechlin (northeastern Germany) substantially differ from those of total bacteria and consist of Alpha-, Beta-, Gamma-, Deltaproteobacteria, Actinobacteria, Candidatus OP10 and Chloroflexi. AGB populations with different BrdU-fluorescence intensities and cell sizes represented different phylotypes suggesting that single-cell growth potential varies at the taxon level. NAG incubation experiments demonstrated that a variety of widespread taxa related to Alpha-, Beta-, Gammaproteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, Planctomycetes, Spirochaetes, Verrucomicrobia and Chloroflexi actively grow in the presence of NAG. The BrdU-FACS approach enables detailed phylogenetic studies of AGB and, thus, to identify those phylotypes which are potential key players in aquatic DOM cycling. [ABSTRACT FROM AUTHOR]

Although aquatic and parasitic fungi have been well known for more than 100 years, they have only recently received increased awareness due to their key roles in microbial food webs and biogeochemical cycles. There is growing evidence indicating that fungi inhabit a wide range of marine habitats, from the deep sea all the way to surface waters, and recent advances in molecular tools, in particular metagenome approaches, reveal that their diversity is much greater and their ecological roles more important than previously considered. Parasitism constitutes one of the most widespread ecological interactions in nature, occurring in almost all environments. Despite that, the diversity of fungal parasites, their ecological functions, and, in particular their interactions with other microorganisms remain largely speculative, unexplored and are often missing from current theoretical concepts in marine ecology and biogeochemistry. In this review, we summarize and discuss recent research avenues on parasitic fungi and their ecological potential in marine ecosystems, e.g., the fungal shunt, and emphasize the need for further research. [ABSTRACT FROM AUTHOR]

: Algal tests have developed into routine tools for testing toxicity of pollutants in aquatic environments. Meanwhile, in addition to algal growth rates, an increasing number of fluorescence based methods are used for rapid and sensitive toxicity measures. The present study stresses the suitability of delayed fluorescence (DF) as a promising parameter for biotests. DF is based on the recombination fluorescence at the reaction centre of photosystem II, which is emitted only by photosynthetically active cells. We analyzed the effects of three chemicals (3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), 3,5 Dichlorophenol (3,5 DCP) and copper) on the shape of the DF decay kinetics for potential use in phytoplankton toxicity tests. The short incubation tests were done with four phytoplankton species, with special emphasis on the cyanobacterium Microcystis aeruginosa. All species exhibited a high sensitivity to DCMU, but cyanobacteria were more affected by copper and less by 3,5 DCP than the tested green algae. Analyses of changes in the DF decay curve in response to the added chemicals indicated the feasibility of the DF decay approach as a rapid and sensitive testing tool. [ABSTRACT FROM AUTHOR]

Chitin is a polymer of major importance in aquatic environments. We report on a new chitin- staining method for environmental samples. Major advantages of this method are (i) its high specificity and (ii) its suitability for combination with general stains, such as 4',6-diamidino-2-phenylindole (DAPI), or taxa-specific methods, such as fluorescence in situ hybridization (FISH). This method lets aquatic mycologists explore basal fungal lineages directly in situ, identify their hosts, occurrence and evolutionary traits. [ABSTRACT FROM AUTHOR]

Associated heterotrophic bacteria alter the microenvironment of cyanobacteria and potentially influence cyanobacterial development. Therefore, we studied interactions of the unicellular freshwater cyanobacterium Microcystis aeruginosa with heterotrophic bacteria. The associated bacterial community was greatly driven by temperature as seen by DNA fingerprinting. However, the associated microbes also closely interacted with the cyanobacteria indicating changing ecological consequence of the associated bacterial community with temperature. Whereas concentration of dissolved organic carbon in cyanobacterial cultures changed in a temperature-dependent manner, its quality greatly varied under the same environmental conditions, but with different associated bacterial communities. Furthermore, temperature affected quantity and quality of cell-bound microcystins, whereby interactions between M. aeruginosa and their associated community often masked this temperature effect. Both macro- and microenvironment of active cyanobacterial strains were characterized by high pH and oxygen values creating a unique habitat that potentially affects microbial diversity and function. For example, archaea including 'anaerobic' methanogens contributed to the associated microbial community. This implies so far uncharacterized interactions between Microcystis aeruginosa and its associated prokaryotic community, which has unknown ecological consequences in a climatically changing world. [ABSTRACT FROM AUTHOR]

Parasites form an integral part of food webs, however, they are often ignored in classic food web theory or limited to the investigation of trophic transmission pathways. Specifically, direct consumption of parasites by nonhost predators is rarely considered, while it can contribute substantially to energy flow in food webs. In aquatic systems, chytrids constitute a major group of fungal parasites whose free‐living infective stages (zoospores) form a highly nutritional food source to zooplankton. Thereby, the consumption of zoospores can create an energy pathway from otherwise inedible phytoplankton to zooplankton ("mycoloop"). This parasite‐mediated energy pathway might be of special importance during phytoplankton blooms dominated by inedible or toxic primary producers like cyanobacteria, which are on the rise with eutrophication and global warming. We theoretically investigated community dynamics and energy transfer in a food web consisting of an edible nonhost and an inedible host phytoplankton species, a parasitic fungus, and a zooplankton species grazing on edible phytoplankton and fungi. Food web dynamics were investigated along a nutrient gradient contrasting nonadaptive zooplankton species representative for filter feeders like cladocerans and zooplankton with the ability to actively adapt their feeding preferences like many copepod species. Overall, the importance of the mycoloop for zooplankton increases with nutrient availability. This increase is smooth for nonadaptive consumers. For adaptive consumers, we observe an abrupt shift from an almost exclusive preference for edible phytoplankton at low nutrient levels to a strong preference for parasitic fungi at high nutrient levels. The model predicts that parasitic fungi could contribute up to 50% of the zooplankton diet in nutrient‐rich environments, which agrees with empirical observations on zooplankton gut content from eutrophic systems during blooms of inedible diatoms or cyanobacteria. Our findings highlight the role of parasite‐mediated energy pathways for predictions of energy flow and community composition under current and future environmental change. [ABSTRACT FROM AUTHOR]

The prevailing paradigm in aquatic science is that microbial methanogenesis happens primarily in anoxic environments. Here, we used multiple complementary approaches to show that microbial methane production could and did occur in the well-oxygenated water column of an oligotrophic lake (Lake Stechlin, Germany). Oversaturation of methane was repeatedly recorded in the well-oxygenated upper 10 m of the water column, and the methane maxima coincided with oxygen oversaturation at 6 m. Laboratory incubations of unamended epilimnetic lake water and inoculations of photoautotrophs with a lake-enrichment culture both led to methane production even in the presence of oxygen, and the production was not affected by the addition of inorganic phosphate or methylated compounds. Methane production was also detected by in-lake incubations of lake water, and the highest production rate was 1.8-2.4 nM~h-1 at 6 m, which could explain 33-44% of the observed ambient methane accumulation in the same month. Temporal and spatial uncoupling between methanogenesis and methanotrophy was supported by field and laboratory measurements, which also helped explain the oversaturation of methane in the upper water column. Potentially methanogenic Archaea were detected in situ in the oxygenated, methane-rich epilimnion, and their attachment to photoautotrophs might allow for anaerobic growth and direct transfer of substrates for methane production. Specific PCR on mRNA of the methyl coenzyme M reductase A gene revealed active methanogenesis. Microbial methane production in oxygenated water represents a hitherto overlooked source of methane and can be important for carbon cycling in the aquatic environments and water to air methane flux. [ABSTRACT FROM AUTHOR]

Pronounced rises in frequency of toxic cyanobacterial blooms are recently observed worldwide, particularly when temperatures increase. Different strains of cyanobacterial species vary in their potential to produce toxins but driving forces are still obscure. Our study examines effects of hydrogen peroxide on toxic and non-toxic (including a non-toxic mutant) strains of M. aeruginosa. Here we show that hydrogen peroxide diminishes chlorophyll a content and growth of cyanobacteria and that this reduction is significantly lower for toxic than for non-toxic strains. This indicates that microcystins protect from detrimental effects of oxygen radicals. Incubation of toxic and non-toxic strains of M. aeruginosa with other bacteria or without (axenic) at three temperatures (20, 26 and 32uC) reveals a shift toward toxic strains at higher temperatures. In parallel to increases in abundance of toxic (i.e. toxin gene possessing) strains and their actual toxin expression, concentrations of microcystins rise with temperature, when amounts of radicals are expected to be enhanced. Field samples from three continents support the influence of radicals and temperature on toxic potential of M. aeruginosa. Our results imply that global warming will significantly increase toxic potential and toxicity of cyanobacterial blooms which has strong implications for socio-economical assessments of global change. [ABSTRACT FROM AUTHOR]

Cyanobacterial blooms represent a nutritious niche for associated bacteria including potential pathogens for humans as well as livestock. We investigated bacterial community composition associated with Microcystis sp. using different approaches: batch experiments on Microcystis sp. or its enriched exudates, field enclosures (dialysis bags) and field sampling during natural blooms in freshwaters. Bacterial community composition associated with Microcystis sp. differed significantly with temperature, bacterial source community and number of incubated cyanobacterial strains. Interestingly, Actinobacteria of the AcI cluster were only present in the 20°C treatments and disappeared at higher incubation temperatures. Moreover, Archaea were present in all field samples but did not show any regional patterns, which is consistent with bacteria. Absence of Archaea in the experimental treatments indicates reduced growth under experimental conditions. In contrast, members of the genus Sphingomonas ( Alphaproteobacteria), which includes species known as human pathogens, occurred in almost all samples. Thus Sphingomonadales seem to be an integral element of Microcystis sp. blooms - even affecting concentrations of microcystins as a result of their breakdown of the toxins. Depending on environmental conditions such as temperature, light, currents and nutrients, the role of heterotrophic Bacteria associated with Cyanobacteria can greatly vary by either increasing (pathogens) or decreasing (breakdown of toxins) health risks caused by mass developments of potentially toxic Cyanobacteria. [ABSTRACT FROM AUTHOR]

Summary In recent years, microbial ecology has developed from a peripheral discipline into a central field of microbiology. This change in state and perception is mainly driven by a rapid development of methods applied in the manifold fields related to microbial ecology. In biogeochemistry, for example, the use of high-resolution techniques such as FT-ICR-MS (Fourier transform ion cyclotron mass spectroscopy) has uncovered an enormous diversity and complexity of natural organic matter produced or degraded microbially either in dissolved or particulate forms. On the other hand, the introduction of high-throughput sequencing methods, such as 454 pyrosequencing, in combination with advances in bioinformatics allows for studying the bacterial diversity in natural samples circumventing cultivation dependent approaches. These new molecular tools enable in depth studies on single-cell genomes, distinct populations or even metacommunities. In combination with metatranscriptome and proteome studies it is for the first time possible to simultaneously unravel the structure and function of complex communities in situ. These technique-derived findings have, on the one hand, dramatically increased our knowledge on the vast diversity and complexity of bacterial habitats and, on the other hand, on phylogentic diversity and physiological responses of natural bacterial communities to their environment. However, until now microbial ecology is lacking an ecologically relevant species definition and useful tools for the identification of ecologically coherent taxa. Studies on intra- and interspecies interactions even with higher organisms demonstrate that bacteria can rapidly adapt to temporal and spatial changes in their environment. Aquatic bacteria have optimized and dramatically expanded their living space by efficient exploitation of organic matter point sources such as particles/aggregates and higher organisms. Although it is evident that particles/aggregates and organisms such as phytoplankton are 'hotspots' for microbial growth and transformation processes, it has not affected sampling strategies of aquatic microbial ecologists, who often focus solely on the free-living bacterial fractions and a priori exclude higher organisms by non-representative water sampling. Therefore, aquatic microbial ecologists have largely overlooked the fact that many aquatic bacteria may possess a complex lifestyle and frequently alternate between a free-living and a surface-associated stage. Here, I propose that modern concepts in aquatic microbial ecology should take into account the high chemical diversity and spatio-temporal variability of the bacterial environment. Interactions of aquatic bacteria with surfaces including living organisms are the key to understanding their physiological adaptations and population dynamics, as well as their contribution to biogeochemical cycles. New sampling strategies and theoretical concepts are needed in aquatic microbial ecology to access the whole spectrum of bacterial lifestyles and their ecological and evolutionary consequences. [ABSTRACT FROM AUTHOR]

Photolysis of dissolved organic matter (DOM) leads to contrasting effects on bacterioplankton dynamics, i.e. stimulation and inhibition of bacterial activity. In particular, the role of short-lived reactive oxygen species (ROS), e.g. singlet oxygen (O), in altering microbial activity and species composition has scarcely been investigated. Therefore, we have artificially increased the natural rate of O formation in short-term (∼4 h) in situ and long-term (72 h) laboratory incubations of surface water samples from a humic acid-rich lake. Denaturing gradient gel electrophoresis (DGGE) patterns revealed significant changes in occurrence of abundant bacterioplankton phylotypes upon O exposure. Cluster analysis of DGGE patterns showed that a moderate increase in O exposure leads to similar changes in different years indicating the establishment of bacterial communities adapted to O exposure. Bacterioplankton phylotypes favoured under these conditions belonged to Betaproteobacteria of the beta II cluster (e.g. Polynucleobacter necessarius) and the beta I cluster related to Limnohabitans (R-BT subcluster) as well as Alphaproteobacteria affiliated to Novosphingobium acidiphilum. In contrast, Actinobacteria of the freshwater acI-B cluster were sensitive even against moderate O exposure. We conclude that O exposure due to DOM photolysis represents an important natural selective factor affecting bacterial species dynamics in aquatic ecosystems in many ways. [ABSTRACT FROM AUTHOR]

Microorganisms and zooplankton are both important components of aquatic food webs. Although both inhabit the same environment, they are often regarded as separate functional units that are indirectly connected through nutrient cycling and trophic cascade. However, research on pathogenic and nonpathogenic bacteria has shown that direct association with zooplankton has significant influences on the bacteria's physiology and ecology. We used stratified migration columns to study vertical dispersal of hitchhiking bacteria through migrating zooplankton across a density gradient that was otherwise impenetrable for bacteria in both upward and downward directions (conveyor-belt hypothesis). The strength of our experiments is to permit quantitative estimation of transport and release of associated bacteria: vertical migration of Daphnia magna yielded an average dispersal rate of 1.3 x 10-5.cells.Daphnia-1. migration cycle-1 for the lake bacterium Brevundimonassp. Bidirectional vertical dispersal by migrating D. magna was also shown for two other bacterial species, albeit at lower rates. The prediction that diurnally migrating zooplankton acquire different attached bacterial communities from hypolimnion and epilimnion between day and night was subsequently confirmed in our field study. In mesotrophic Lake Nehmitz, D. hyalina showed pronounced diel vertical migration along with significant diurnal changes in attached bacterial community cornposition. These results confirm that hitchhiking on migrating animals can be an important mechanism for rapidly relocating microorganisms, including pathogens, allowing them to access otherwise inaccessible resources. [ABSTRACT FROM AUTHOR]

Bacterial incorporation of glucose, leucine, acetate and 4-hydroxybenzoic acid (HBA) was investigated in an artificially divided humic lake (Grosse Fuchskuhle, Germany). Two basins with contrasting influx of allochthonous organic carbon were sampled during late summer stratification (oxic and anoxic layers) and after autumn mixing. High total and cell-specific incorporation rates were observed for glucose and HBA in stratified and mixed waters respectively, but only a small fraction of bacteria visibly incorporated HBA. The oxic layer of the more humic-rich basin featured a significantly lower fraction of glucose incorporating cells and substantially higher proportions of acetate assimilating bacteria. Niche differentiation was observed in two betaproteobacterial populations: cells affiliated with the Polynucleobacter C subcluster efficiently incorporated acetate but little glucose, whereas the opposite was found for members of the R-BT065 clade. By contrast, leucine incorporation was variable in both taxa. Considering the high concentrations and rapid photochemical generation of organic acids in humic waters our results may help to explain the success of the Polynucleobacter C lineage in such habitats. Specific substrate or habitat preferences were also present in three subgroups of the actinobacterial acI lineage: The numerically dominant clade in oxic waters (acI-840-1) was absent in the anoxic zone and did not incorporate acetate. A second group (acI-840-2) was found both in the epi- and hypolimnion, whereas the third one (acI-840-3) only occurred in anoxic waters. Altogether our results suggest a constitutive preference for some substrates versus an adaptive utilization of others in the studied microbial groups. [ABSTRACT FROM AUTHOR]

Bacterial community compositions (BCC) associated with the cladoceran Bosmina coregoni and the cyclopoid copepod Thermocyclops oithonoides in oligotrophic Lake Stechlin versus eutrophic Lake Dagow (northeastern Germany) were compared using molecular techniques. We also transplanted the zooplankton from their native lake to the other lake, and studied changes in their associated BCC as a result of the modified ambient environment. Bacterial community composition associated with B. coregoni was quite conservative between the oligotrophic and eutrophic lakes, and most of the bacteria belonged to Alpha- and Betaproteobacteria. In contrast, BCC associated with T. oithonoides was highly variable and dependent on the environment, and Betaproteobacteria and Bacteroidetes were the most represented among the bacteria. Thermocyclops oithonoides from the oligotrophic lake was more able to retain its bacteria after being transplanted to the eutrophic lake than vice versa. This suggests that bacteria in oligotrophic water were more firmly attached to the copepod and better in resisting environmental fluctuations than those in eutrophic water. [ABSTRACT FROM AUTHOR]

Two γ-Proteobacteria strains, that is, HP1 and HP9, which both produce a diffusible deep blue pigment, were isolated from the German Wadden Sea and from the Øresund, Denmark, respectively. Both strains affiliate with the genus Rheinheimera. Small amounts of the pigment could be extracted from HP1 grown in a 50 L fermenter and were purified chromatographically. Chemical analysis of the pigment including NMR and mass spectrometry led to a molecular formula of C34H56N4O4 (m.w. 584.85) which has not yet been reported in literature. The molecule is highly symmetrically and consists of two heterocyclic halves to which aliphatic side chains are attached. The pigment has been named glaukothalin due to its blue color and its marine origin (glaukos, gr. = blue, thalatta, gr. = sea). Production of glaukothalin on MB2216 agar plates by our Rheinheimera strains is affected in the presence of other bacterial strains either increasing or decreasing pigment production. The addition of a single amino acid, arginine (5 gl-1), greatly increases pigment production by our Rheinheimera strains. Even though the production of glaukothalin leads to inhibitory activity against three bacterial strains from marine particles, our Rheinheimera isolates are inhibited by various bacteria of different phylogenetic groups. The ecological role of glaukothalin production by Rheinheimera strains, however, remains largely unknown. [ABSTRACT FROM AUTHOR]

Bacteria growing on marine particles generally have higher densities and cell-specific activities than free-living bacteria. Since rapidity of phage adsorption is dependent on host density, while infection productivity is a function of host physiological status, we hypothesized that marine particles are sites of elevated phage production. In the present study, organic-matter-rich agarose beads and a marine phage–host pair ( Cellulophaga sp., ΦSM) were used as a model system to examine whether bacterial colonization of particles increases phage production. While no production of phages was observed in plain seawater, the presence of beads enhanced attachment and growth of bacteria, as well as phage production. This was observed because of extensive lysis of bacteria in the presence of beads and a subsequent increase in phage abundance both on beads and in the surrounding water. After 12 h, extensive phage lysis reduced the density of attached bacteria; however, after 32 h, bacterial abundance increased again. Reexposure to phages and analyses of bacterial isolates suggested that this regrowth on particles was by phage-resistant clones. The present demonstration of elevated lytic phage production associated with model particles illustrates not only that a marine phage has the ability to successfully infect and lyse surface-attached bacteria but also that acquisition of resistance may affect temporal phage–host dynamics on particles. These findings from a model system may have relevance to the distribution of phage production in environments rich in particulate matter (e.g., in coastal areas or during phytoplankton blooms) where a significant part of phage production may be directly linked to these nutrient-rich “hot spots.” [ABSTRACT FROM AUTHOR]

Our novel approach for taxonomic identification of uncultured bacteria harboring specific physiological features in complex environmental samples combines cell collection by laser microdissection and subsequent DNA analysis. The newly developed approach was successfully tested for collection and phylogenetic characterization of polyphosphate-accumulating bacteria in activated sludge and lake sediment. [ABSTRACT FROM AUTHOR]

We examined in situ abundance and activities of the major bacterial groups in the two most distinct compartments of experimentally divided Lake Grosse Fuchskuhle (Germany). The selected south-west (SW) and north-east basin (NE) differ substantially in their major chemical and biological parameters that potentially influence the dynamics and composition of microbial communities. Water from the basins were incubated in dialysis bags, which allowed for a relatively free exchange of nutrients, limiting solutes and low molecular organic matter but fully prevented exchange of organisms. To investigate the effect of top-down and bottom-up manipulations three size fractions of water samples were produced: (i) unfiltered, (ii) pre-filtered through 5.0 μm pore size membranes to remove large particles, as well as grazers and (iii) pre-filtered through 0.8 μm filters to remove all potential bacterivores. One set of dialysis bags was either incubated in acidic SW (rich in humic matter) or in almost neutral NE basin whereas a second set was transferred from the SW to the NE basin and vice versa. Our study revealed pronounced differences in growth rates among the major bacterial groups in relation to the treatments. Members of the Betaproteobacteria, in particular of the subgroup targeted by the BETA2-870 probe, were highly abundant in both basins, and most of them belonged to the Polynucleobacter necessesarius subcluster PnecC. Their specific growth rates surprisingly increased in all treatments when being transplanted into the acidic SW basin, indicating that pH and humic substances greatly affected growth of this particular group in the lake. In contrast, members of the Sphingobacteria/Flavobacteria group of the Bacteroidetes (both basins) as well as Actinobacteria (SW basin) were less abundant, especially in the presence of flagellates (< 5.0 μm treatments). However, because of their extremely low initial numbers, grazing of heterotrophic nanoflagellates mostly controlled only a small part of the bacterial production (≤ 12%). [ABSTRACT FROM AUTHOR]

Iron availability in the ocean has been shown to affect the growth and production of phytoplankton and free-living bacteria. A large fraction of marine bacteria are specialized in colonizing and living on particles and aggregates, but the effects of iron limitation on these bacteria are not fully known. We conducted laboratory experiments to study the effects of iron availability on particle colonization behavior, motility, and enzymatic activities of 4 strains of marine bacteria. Iron depletion reduced the bacterial particle colonization rate by 1.7%–43.1%, which could be attributed to reduced swimming speeds in 2 of the 4 strains. Protease activity was not affected by iron availability. However, attached bacteria did show higher protease activities than their free counterparts. Our results suggest that iron limitation in the ocean could in some cases reduce bacteria–particle interactions by reducing bacterial motility and colonization rate. [ABSTRACT FROM AUTHOR]

Marine snow aggregates are microbial hotspots that support high bacterial abundance and activities. We conducted laboratory experiments to compare cell-specific bacterial protein production (BPP) and protease activity between free-living and attached bacteria. Natural bacterial assemblages attached to model aggregates (agar spheres) had threefold higher BPP and two orders of magnitude higher protease activity than their free-living counterpart. These observations could be explained by preferential colonization of the agar spheres by bacteria with inherently higher metabolic activity and/or individual bacteria increasing their metabolism upon attachment to surfaces. In subsequent experiments, we used four strains of marine snow bacteria isolates to test the hypothesis that bacteria could up- and down-regulate their metabolism while on and off an aggregate. The protease activity of attached bacteria was 10–20 times higher than that of free-living bacteria, indicating that the individual strains could increase their protease activity within a short time (2 h) upon attachment to surfaces. Agar spheres with embedded diatom cells were colonized faster than plain agar spheres and the attached bacteria were clustered around the agar-embedded diatom cells, indicating a chemosensing response. Increased protease activity and BPP allow attached bacteria to quickly exploit aggregate resources upon attachment, which may accelerate remineralization of marine snow and reduce the downward carbon fluxes. [ABSTRACT FROM AUTHOR]

Aggregation of algae, mainly of diatoms, is an important process in marine pelagic systems, often terminating phytoplankton blooms and leading to the sinking of particulate organic matter in the form of marine snow. This process has been studied extensively, but the specific role of heterotrophic bacteria has largely been neglected, mainly because field studies and most experimental work were performed under non-axenic conditions. We tested the hypothesis that algae–bacteria interactions are instrumental in aggregate dynamics and organic matter flux. A series of aggregation experiments has been carried out in rolling tanks with two marine diatoms typical of temperate regions ( Skeletonema costatum and Thalassiosira rotula) in an axenic treatment and one inoculated with marine bacteria. Exponentially growing S. costatum and T. rotula exhibited distinctly different aggregation behavior. This was reflected by their strikingly different release of dissolved organic matter (DOM), transparent exopolymer particles (TEP) and protein-containing particles (CSP), as well as their bacterial biodegradability and recalcitrance. Cells of S. costatum aggregated only little and their bacterial colonization remained low. Dissolved organic matter, TEP and CSP released by this alga were largely consumed by free-living bacteria. In contrast, T. rotula aggregated rapidly and DOM, TEP and CSP released resisted bacterial consumption. Experiments conducted with T. rotula cultures in the stationary growth phase, however, showed rapid bacterial colonization and decomposition of algal cells. Our study highlights the importance of heterotrophic bacteria to control the development and aggregation of phytoplankton in marine systems. [ABSTRACT FROM AUTHOR]

The phylogenetic diversity and seasonal dynamics of freshwater Actinobacteria populations in four limnologically different lakes of the Mecklenburg-Brandenburg Lake District (northeastern Germany) were investigated. Fluorescence in situ hybridization was used to determine the seasonal abundances and dynamics of total Actinobacteria (probe HGC69a) and the three actinobacterial subclusters ad, ad-A, and ad-B (probes AcI-852, AcI-840-1, and AcI-840-2). Seasonal means of total Actinobacteria abundances in the epilimnia of the lakes varied from 13 to 36%, with maximum values of 30 to 58%, of all DAPI (4′,6′'-diamidino-2.phenylindole)-stained cells. Around 80% of total Actinobacteria belonged to the ad cluster. The two subclusters ad-A and ad-B accounted for 60 to 91% of the ad cluster and showed seasonal means of 49% (ad-B) and 23% (ad-A) in relation to the ad cluster. Total Actinobacteria and members of the clusters ad and ad-B showed distinct seasonal changes in their absolute abundances, with maxima in late spring and fall/winter. In eight clone libraries constructed from the lakes, a total of 76 actinobacterial 16S rRNA gene sequences were identified from a total of 177 clones. The majority of the Actinobacteria sequences belonged to the ad and aclV cluster. Several new clusters and subclusters were found (acSTL, scBl-4, and acIVA-D). The majority of all obtained 16S rRNA gene sequences are distinct from those of already-cultured freshwater Actinobacteria. [ABSTRACT FROM AUTHOR]

To date no study exists that directly addresses changes in dynamics of heterotrophic bacteria in surface waters in relation to partial pressure of CO2 (pCO2). Therefore, we studied the effect of changes in pCO2 on bacterial abundance and activities by using mesocosms with different pCO2 levels (∼190, ∼370, and ∼700 ppmV, representing past, present-day, and future atmospheric pCO2, respectively). Abundance of total bacteria did not differ with increasing pCO2 throughout the whole study period, whereas bacterial protein production (BPP) was highest at highest pCO2. This effect was even more pronounced for cell-specific production rates, especially those of attached bacteria, which were up to 25 times higher than those of free bacteria. During the breakdown of the bloom, however, the abundance of both free and attached bacteria was significantly increased with pCO2. Differences in bacterial growth rate (μ) were smaller than those of BPP, but both μ and BPP of attached bacteria were elevated under high pCO2. Averages of total protease as well as α- and β-glucosidase activities were highest at elevated pCO2 levels, but a statistically significant dependence on pCO2 was only evident for protease activity. There is a measurable but indirect effect of changes in pCO2 on bacterial activities that are mainly linked to phytoplankton and presumably particle dynamics. [ABSTRACT FROM AUTHOR]

Abstract: Exopolymeric substances (EPS) isolated from a pure culture of the marine bacterium Marinobacter sp. and the marine diatom Skeletonema costatum (axenic) were partially purified, chemically characterized and used as dissolved organic matter (DOM) for the production of macroaggregates. The role of organic particles such as transparent exopolymeric particles (TEP) and Coomassie stained particles (CSP) in the production of macroaggregates was experimentally assessed. Three experimental rolling tanks containing sterile medium with: (1) EPS, (2) EPS+live diatom cells and (3) EPS+killed bacteria, and three control tanks without any added EPS were used for macroaggregate production. Changes in abundance and average size of macroaggregates were monitored using image analysis, whereas TEP and CSP were enumerated microscopically. In the presence of microbial EPS, macroaggregates of a size of 23–35mm2 were produced. Aggregate size and abundance considerably varied with both time and source of EPS. No correlation was observed for macroaggregate size and abundance with either TEP or CSP. One-way ANOVA demonstrated significant differences in the variance of particle abundance and size in tanks having only EPS or EPS in combination with live diatom cells. Our data suggest that production of macroaggregates was influenced by polymer chemistry and surface properties of colliding particles, whereas TEP and CSP concentrations were influenced by molecular weight of EPS and the presence of growing cells. Interestingly, macroaggregates were formed in the near absence of TEP and CSP, highlighting the role of other unknown processes in the transformation of DOM to particulate organic matter (POM) in aquatic environments. [Copyright &y& Elsevier]

We examined bacterial dynamics in batch cultures of two axenic marine diatoms (Thalassiosira rotulaandSkeletonema costatum). The axenic diatoms were inoculated with natural bacterial assemblages and monitored by 4,6-diamidino-2-phenolindole (DAPI) counts, denaturing gradient gel electrophoresis (DGGE) with subsequent analysis of excised, sequenced 16S rRNA gene fragments, and fluorescencein situhybridization (FISH) with group-specific 16S rRNA oligonucleotide probes. Our results show that algal growth exhibited pronounced differences in axenic treatments and when bacteria were present. Bacterial abundance and community structure greatly depended on species, growth and physiological status of even closely related algae. Free-living and phytoplankton-associated bacteria were very different from each other and were dominated by distinct phylogenetic groups. The diatom-associated bacteria mainly belonged to theFlavobacteria– Sphingobacteriagroup of the Bacteroidetes phylum whereas free-living bacteria, which were rather similar in both cultures, comprised mainly of members of theRoseobacter group of α-Proteobacteria. Presence and disappearance of specific bacteria during algal growth indicated pronounced differences in environmental conditions over time and selection of bacteria highly adapted to the changing conditions. Tight interactions between marine bacteria and diatoms appear to be important for the decomposition of organic matter and nutrient cycling in the sea. [ABSTRACT FROM AUTHOR]

Tidal flat ecosystems are highly dynamic environments with tremendous short-term and long-term changes in physical, chemical, and biological properties. We measured salinity, temperature, oxygen, dry weight (dry wt), inorganic (PIC) and organic carbon (POC) fractions of suspended particulate matter (SPM), and chlorophyll a (Chl a); counted numbers of free-living and particle-associated bacteria; and measured dissolved amino acids and carbohydrates, and ectoenzymatic activities throughout tidal cycles in the Spiekeroog tidal flat system of the German Wadden Sea in November 1999 and May 2000. Bacterial production was measured only in May 2000. resuspension, as indicated by increased amounts of SPM, PIC, and POC, mainly controlled bacterial dynamics and led to enhanced numbers of aggregate-associated bacteria. In contrast, in May, phytoplankton-related processes mainly influenced bacterial dynamics. Increased concentrations of oxygen, Chl a, and dissolved combined neutral monosaccharides resulted in high numbers of free-living bacteria, elevated β-glucosidase activities, and high bacterial production rates. The introduction of foreign water masses, either from the open North Sea or adjacent tidal basins, as reflected by different signatures of SPM and the mole percent composition of particulate combined amino acids, appeared to be a regular event in this highly dynamic system and rapidly changed physical, chemical, and biological processes. [ABSTRACT FROM AUTHOR]

Marine aggregates are densely colonized by bacteria, and inter-specific interactions such as inhibition are important for colonization by aggregate-associated bacteria and thus affect the turnover of organic matter in the sea. In order to study antagonistic activities we carried out inhibition tests with 51 isolates obtained exclusively from aggregates of the German Wadden Sea. 16S rRNA gene sequences of all isolates revealed that 35% of the isolates affiliated with the Flavobacteria/Sphingobacteria group, 24% and 16% with α- and γ-Proteobacteria, respectively, 16% with the Bacillus/Clostridium group, and 10% with Actinobacteria. The relatively high percentage of Gram-positive bacteria may be related to specific features of the Wadden Sea environment. After 11 days of incubation using Burkholder agar diffusion assays the percentage of inhibitory isolates was 54.1% and this decreased to 20.7% after 20 days of incubation but it did not decline for members of the Bacillus/Clostridium group. Inhibitory activity was expressed in strain-specific patterns even though some isolates were closely related according to their 16S rRNA gene sequences. Antagonistic activity was lowest for Flavobacteria/Sphingobacteria (35%) and highest for Actinobacteria (80%). We further examined whether growth of isolates was affected when they were placed on lawns of certain other isolates. In parallel with lowest percentage of inhibitory isolates, highest growth occurred on lawns of the Flavobacteria/Sphingobacteria group whereas it was lowest on lawns of Actinobacteria and the Bacillus/Clostridium group. The high inhibitory activity of both groups of Gram-positive bacteria fits well with data from chemical screening using matrix-assisted laser desorption ionization time of flight mass spectrometry. Hence, inhibitory activity greatly influences inter-specific interactions and may impact microbial degradation and remineralization of particulate organic matter in aquatic environments. [Copyright &y& Elsevier]

Marine particles in the ocean are exposed to diverse bacterial communities, and colonization and growth of attached bacteria are important processes in the degradation and transformation of the particles. In an earlier study, we showed that the initial colonization of model particles by individual bacterial strains isolated from marine aggregates was a function of attachment and detachment. In the present study, we have investigated how this colonization process was further affected by growth and interspecific interactions among the bacteria. Long-term incubation experiments showed that growth dominated over attachment and detachment after a few hours in controlling the bacterial population density on agar particles. In the absence of grazing mortality, this growth led to an equilibrium population density consistent with the theoretical limit due to oxygen diffusion. Interspecific interaction experiments showed that the presence of some bacterial strains ("residents") on the agar particles either increased or decreased the colonization rate of other strains ("newcomers"). Comparison between an antibiotic-producing strain and its antibiotic-free mutant showed no inhibitory effect on the newcomers due to antibiotic production. On the contrary, hydrolytic activity of the antibiotic-producing strain appeared to benefit the newcomers and enhance their colonization rate. These results show that growth- and species-specific interactions have to be taken into account to adequately describe bacterial colonization of marine particles. Changes in colonization pattern due to such small-scale processes may have profound effects on the transformation and fluxes of particulate matter in the ocean. [ABSTRACT FROM AUTHOR]

Examines the production of communication signals involved in quorum sensing by gram-negative bacteria associated with marine snow. Isolation of marine bacteria; Synthesis of acylated homoserine lactones by Roseobacter; Properties of bacterial strains.

Examines the quantification of bacterial colonization of sinking aggregates. Estimation of diffusion coefficients; Properties of bacterial strains; Types of colonization patterns.

Seeks to develop a simple, rapid method for demonstrating flagellation of bacteria using the fluorescent protein stain NanoOrange. Enhancement of fluorescence; Detection of flagella; NanoOrange staining; Motility and flagellation of bacterial isolates; Staining of nonmotile, nonflagellated Escherichia coli.

Background: Riverine ecosystems are one of the most important reservoirs of antibiotic resistance genes (ARGs) in the environment, but the occurrence and controlling factors of ARG distribution in different habitats of riverine ecosystems remain poorly understood. In this study, a metagenomic approach was used to characterize ARG types and their abundance in different habitats (rhizosphere soil, surface bulk soil, bottom bulk soil, and sediment) of riverine ecosystems in eastern China. Sampling sites were located along different rivers of eastern China, which are geographically isolated. Differences in bacterial communities, mobile genetic elements (MGEs), pattern and intensity of human activities, climate, and other environmental factors at the sampling sites and habitats were expected to affect ARG occurrence. Results: ARGs were observed with high variations in diversity (44–206 subtypes) and abundance (6.85–105.68 ×/Gb). There were significant south-north differences in ARG occurrence in the same habitat, except for surface bulk soil. And the significant difference was found in ARGs among four southern habitats. South–north differences in ARGs of the same habitat were mainly attributed to the combination of different occurrence frequencies and habitat selections of ARGs. Differences in ARG profiles among the four habitats in the south and the north were both mainly attributed to the different occurrence frequencies of ARGs. Bacterial communities and MGEs (Mobile genetic elements) could account for the observed variance in the resistome of riverine ecosystems across eastern China. The co-occurrences of specific ARGs with bacterial communities and MGEs were more frequent at the northern sampling sites than in the south, and co-occurrence patterns (i.e. ARGs and bacterial communities or ARGs and MGEs) varied between the habitats. Moreover, building land in all habitats, except bulk soils, showed significant positive correlations with ARG abundance. Conclusion: This study reveals a high variance in the resistome of riverine ecosystems in eastern China and its controlling factors. We appeal to the importance of assessment of ARGs in the riverine ecosystem and the need for future prevention and intervention of ARG spread. [ABSTRACT FROM AUTHOR]

Conventional agricultural practices negatively impact soil biodiversity, carbon stocks, and greenhouse gas emissions in ways that make them unsustainable for supporting future supply of food and fiber. Better management of agrobiodiversity will likely play a critical role in transitioning toward more sustainable practices. In particular, innovation and developments targeting the aboveground and belowground components of agroecosystems should be informed by frameworks and approaches that harness the--in particular functional--diversity of complex microbial communities. Here, we review and discuss microbial trait-based approaches that will help us understand and steer agroecosystem functioning in the face of global change. We highlight how trait-based approaches can improve agricultural practices related to soil functioning (e.g., soil fertility and aggregation); climate regulation (e.g., carbon storage and greenhouse gas emissions) and adaptation to climate change; plant health; and reduction of contaminant-related hazards for human health. We also consider how microbial trait-based approaches can be used as a tool to improve cultivated plant performance through artificial selection and microbiome engineering. Last, we discuss the inherent obstacles associated with the development and implementation of trait-based approaches owing to strong interactions within microbial communities and linkages between plants and the soil environment. Despite these obstacles, microbial trait-based approaches hold promise for the sustainable management of agricultural ecosystems needed to feed and nourish a rapidly growing human population. [ABSTRACT FROM AUTHOR]

The phosphorus (P) concentration is increasing in parts of the Baltic Sea following the spring bloom. The fate of this excess P-pool is an open question, and here we investigate the role of microbial degradation processes in the excess P assimilation phase. During a 17-day-long mesocosm experiment in the southwest Finnish archipelago, we examined nitrogen, phosphorus, and carbon acquiring extracellular enzyme activities in three size fractions (<0.2, 0.2–3, and >3 µm), bacterial abundance, production, community composition, and its predicted metabolic functions. The mesocosms received carbon (C) and nitrogen (N) amendments individually and in combination (NC) to distinguish between heterotrophic and autotrophic processes. Alkaline phosphatase activity occurred mainly in the dissolved form and likely contributed to the excess phosphate conditions together with grazing. At the beginning of the experiment, peptidolytic and glycolytic enzymes were mostly produced by free-living bacteria. However, by the end of the experiment, the NC-treatment induced a shift in peptidolytic and glycolytic activities and degradation of phosphomonoesters toward the particle-associated fraction, likely as a consequence of higher substrate availability. This would potentially promote retention of nutrients in the surface as opposed to sedimentation, but direct sedimentation measurements are needed to verify this hypothesis. [ABSTRACT FROM AUTHOR]

Pelagic bacteria can be classified into free‐living and particle‐attached life modes, which either dwell in the water column or attach to suspended particles. Bacteria with a generalist life style, however, can actively shift between these two habitats. Globally increasing densities of natural and artificial particles enhance habitat heterogeneity, with potential consequences for system stability and trophic transfer through aquatic food webs. To better decipher the dynamics of microbial communities, we investigated the influence of adaptive vs. fixed habitat choice on species coexistence for a simplified bacterial community by analyzing a corresponding food web model, consisting of two specialist bacterial prey species (free and attached), a generalist bacterial prey species with the ability to shift between both habitats, and two protist predators, specialized on either water or particle compartment. For simplicity we assume a shared resource pool, considering particles only for colonization but not as a source for nutrients or carbon, that is, inert particles like microplastics or inorganic sediments. The model predicts coexistence on a cyclic attractor between fixed and flexible bacteria, if the costs for adaptive habitat choice can be balanced by adaptation speed. The presence of adaptive prey dampens predator–prey cycle amplitudes, contributing to system stabilization resulting in higher mean predator biomass compared to specialist prey only. Thus, in pelagic microbial systems, flexible habitat choice at the prey level has important implications for system stability and magnitude of energy flow through the microbial loop. [ABSTRACT FROM AUTHOR]

• Taxonomy and phylogeny were tightly correlated with environmental factors. • Rare taxa showed stronger environmental adaptation than abundant taxa. • Dissolved oxygen mediated balance between stochastic and deterministic processes. Deciphering responses of rare versus abundant bacterioplankton to environmental change, crucial for understanding and mitigating of cyanobacterial blooms, is an important but poorly investigated subject. Using MiSeq sequencing, we investigated the taxonomic and phylogenetic diversity of rare and abundant bacterioplankton in eutrophic Lake Nanhu before and after dredging. We estimated environmental breadths and phylogenetic signals of ecological preferences of rare and abundant bacterioplankton, and investigated community function and bacterioplankton assembly processes. Both taxonomic and phylogenic distances of rare and abundant bacterioplankton communities were significantly positively correlated with the dissimilarity of environmental factors. Threshold indicator taxa analysis and Blomberg's K statistic indicated that rare taxa held broader environmental thresholds and stronger phylogenetic signals for ecological traits than abundant taxa. Environmental adaptations of both rare and abundant taxa exhibited distinct changes after dredging. Higher functional redundancy occurred in the abundant compared to the rare bacterioplankton, with functions of rare bacterioplankton decreasing and for the abundant ones increasing after dredging. The null model revealed that dispersal limitation belonging to stochastic processes determined the abundant bacterioplankton community assembly, whereas variable selection belonging to deterministic processes drove the rare one. Rare bacterioplankton was more environmentally constrained than the abundant one. Dissolved oxygen was the decisive factor in determining the balance between stochasticity and determinism in both rare and abundant bacterioplankton. Our study extends our knowledge of environmental adaptation of rare versus abundant bacterioplankton to massive disturbing measures, i.e. dredging, and allows to estimate dredging performance for mitigating cyanobacterial blooms from a molecular ecology viewpoint. Image, graphical abstract [ABSTRACT FROM AUTHOR]

Summary: Marine bacteria rely on phytoplankton exudates as carbon sources (DOCp). Yet, it is unclear to what extent phytoplankton exudates also provide nutrients such as phytoplankton‐derived N and P (DONp, DOPp). We address these questions by mesocosm exudate addition experiments with spent media from the ubiquitous pico‐cyanobacterium Prochlorococcus to bacterial communities in contrasting ecosystems in the Eastern Mediterranean – a coastal and an open‐ocean, oligotrophic station with and without on‐top additions of inorganic nutrients. Inorganic nutrient addition did not lower the incorporation of exudate DONp, nor did it reduce alkaline phosphatase activity, suggesting that bacterial communities are able to exclusively cover their nitrogen and phosphorus demands with organic forms provided by phytoplankton exudates. Approximately half of the cells in each ecosystem took up detectable amounts of Prochlorococcus‐derived C and N, yet based on 16S rRNA sequencing different bacterial genera were responsible for the observed exudate utilization patterns. In the coastal community, several phylotypes of Aureimarina, Psychrosphaera and Glaciecola responded positively to the addition of phytoplankton exudates, whereas phylotypes of Pseudoalteromonas increased and dominated the open‐ocean communities. Together, our results strongly indicate that phytoplankton exudates provide coastal and open‐ocean bacterial communities with organic carbon, nitrogen and phosphorus, and that phytoplankton exudate serve a full‐fledged meal for the accompanying bacterial community in the nutrient‐poor eastern Mediterranean. [ABSTRACT FROM AUTHOR]

The isotopic ratio 18O/16O of dissolved O2 in aquatic systems is affected by the preferential biological uptake of 16O (ε). Studies over the past six decades reveal that during incubation experiments, the isotopic effect of microorganism respiration (εorganism) varies in the range of −18‰ to −22‰. In contrast, natural variations in the deep‐ocean O2 concentration and δ18O levels show a considerably weaker effect (~ −10‰). The differences between these observations have been explained to result from either O2 uptake by sediments or organic particles that, due to diffusion‐limited respiration, are expected to weakly fractionate oxygen isotopes, by mixing processes or by weak fractionation at low temperatures. To gain better insight, we studied oxygen demand and δ18O in the deep, cold hypolimnion of Lake Stechlin between 2018 and 2021 as well as in various laboratory incubations. Our incubation results demonstrate an εorganism of about −24‰. Simple model calculations demonstrate a sediment O2 demand isotope effect (εSOD) of about −8.4‰, and a variated water‐column O2 demand isotope effect (εWOD) which is lower than εorganism, ranging from −13.9‰ in 2019 to −23‰ in 2021. Accompanying experiments indicate that the lower magnitude of εWOD may be related to respiration at organic particles lending to a weaker fractionation effect. Thus, variations in εWOD may reflect a changing partitioning of hypolimnion oxygen uptake between suspended particles and their containing microorganisms. Based on own incubation experiments with Daphnia carcasses, we discuss how possible changes of particle rigidity might influence εWOD. [ABSTRACT FROM AUTHOR]

When oxygen consumption exceeds renewal, anoxic conditions can develop rapidly. The delivery of terrestrial organic matter to inland waters often promotes anoxia by fueling microbial O₂ consumption and increasing the resistance towards convective mixing, as observed in wetland ponds and small lakes. There, and further along its passage through the aquatic network, such dissolved organic matter (DOM) is subject to microbial processing, and the water retention time is known to be a key determinant of its ambient concentration and reactivity. However, in the absence of oxygen, the prevalent biogeochemical conditions markedly shift and so do the processes that modulate and consume organic carbon. Since anoxic waters are ubiquitous components of the land-ocean continuum, we aim to reconcile DOM modifications during its transient residence in anoxic waters with its reactive fate during downstream transport. Here, we present results of a study explicitly assessing the various reaction pathways of DOM in the anoxic water layers of two small north-temperate lakes. We found that increasing residence time in anoxic waters gradually alters the chemical, optical and redox properties of DOM. By monitoring additional metabolism indicators including C mineralization, bacterial production and electron acceptor consumption we were able to gain an improved understanding of the factors that govern the rate of carbon processing in this environment. Our results suggest that contrary to the general perception, anoxia constitutes an environment of continuous carbon turnover that possibly harbors unique DOM processing routes. Specific landscape features that control the exposure of DOM to anoxia during the land-to-ocean transit will be discussed. [ABSTRACT FROM AUTHOR]