Methane Production in Oxic Lake Waters Potentially Increases Aquatic Methane Flux to Air

Active methane production in oxygenated lake waters challenges the long-standing paradigm that microbial methane production occurs only under anoxic conditions and forces us to rethink the ecology and environmental dynamics of this powerful greenhouse gas. Methane production in the upper oxic water layers places the methane source closer to the air–water interface, where convective mixing and microbubble detrainment can lead to a methane efflux higher than that previously assumed. Microorganisms may produce methane in oxic environments by being equipped with enzymes to counteract the effects of molecular oxygen during methanogenesis or using alternative pathways that do not involve oxygen-sensitive enzymes. As this process appears to be influenced by thermal stratification, water transparency, and primary production, changes in lake ecology due to climate change will alter methane formation in oxic water layers, with far-reaching consequences for methane flux and climate feedback

Organic Particles: Heterogeneous Hubs for Microbial Interactions in Aquatic Ecosystems

The dynamics and activities of microbes colonizing organic particles (hereafter particles) greatly determine the efficiency of the aquatic carbon pump. Current understanding is that particle composition, structure and surface properties, determined mostly by the forming organisms and organic matter, dictate initial microbial colonization and the subsequent rapid succession events taking place as organic matter lability and nutrient content change with microbial degradation. We applied a transcriptomic approach to assess the role of stochastic events on initial microbial colonization of particles. Furthermore, we asked whether gene expression corroborates rapid changes in carbon-quality. Commonly used size fractionated filtration averages thousands of particles of different sizes, sources, and ages. To overcome this drawback, we used replicate samples consisting each of 3–4 particles of identical source and age and further evaluated the consequences of averaging 10–1000s of particles. Using flow-through rolling tanks we conducted long-term experiments at near in situ conditions minimizing the biasing effects of closed incubation approaches often referred to as “the bottle-effect.” In our open flow-through rolling tank system, however, active microbial communities were highly heterogeneous despite an identical particle source, suggesting random initial colonization. Contrasting previous reports using closed incubation systems, expression of carbon utilization genes didn’t change after 1 week of incubation. Consequently, we suggest that in nature, changes in particle-associated community related to carbon availability are much slower (days to weeks) due to constant supply of labile, easily degradable organic matter. Initial, random particle colonization seems to be subsequently altered by multiple organismic interactions shaping microbial community interactions and functional dynamics. Comparative analysis of thousands particles pooled togethers as well as pooled samples suggests that mechanistic studies of microbial dynamics should be done on single particles. The observed microbial heterogeneity and inter-organismic interactions may have important implications for evolution and biogeochemistry in aquatic systems

Heterocyst-Specific Transcription of NsiR1, a Non-Coding RNA Encoded in a Tandem Array of Direct Repeats in Cyanobacteria

In response to nitrogen deficiency, some cyanobacteria develop heterocysts, a terminally differentiated cell type, specialized for the fixation of atmospheric nitrogen. In Nostocales, this differentiation process is controlled by two major regulators, NtcA and HetR, but additional unknown factors are likely to be involved as well. In the context of a genome-wide search for potential non-coding RNAs, we identified an array of 12 tandem repeats that is transcribed in large amounts when cells enter conditions that trigger cell differentiation and switch to nitrogen fixation. The main accumulating transcript, which we suggest designating nitrogen stress-induced RNA 1 (NsiR1), has properties similar to regulatory non-coding RNAs. In Anabaena sp. PCC 7120, it is about 60 nt in length, has a very distinct predicted secondary structure, and is expressed very early and transiently after nitrogen step-down. Moreover, its expression requires HetR and NtcA and is restricted to cells that are differentiating into heterocysts, clearly placing NsiR1 within the regulon that controls the switch to nitrogen fixation and heterocyst formation. The genomic arrangement of NsiR1, located upstream of hetF, a gene whose product is involved in heterocyst formation, is conserved in all five Nostocales whose genomes are completely sequenced. Additionally, we detected NsiR1 expression in 19 different heterocyst-forming cyanobacteria. Our data suggest that every repeat is a complete transcriptional unit furnished with a cell-type-specific promoter and a Rho-independent terminator, which gives rise to a very high NsiR1 transcript level. NsiR1 is the first known bacterial non-coding RNA that is specifically upregulated in response to nitrogen step-down. © 2010 Elsevier Ltd

The rate of environmental change as an important driver across scales in ecology

Global change has been predominantly studied from the prism of ‘how much' rather than ‘how fast' change occurs. Associated to this, there has been a focus on environmental drivers crossing a critical value and causing so-called regime shifts. This presupposes that the rate at which environmental conditions change is slow enough to allow the ecological entity to remain close to a stable attractor (e.g. an equilibrium). However, environmental change is occurring at unprecedented rates. Equivalently to the classical regime shifts, theory shows that a critical threshold in rates of change can exist, which can cause rate-induced tipping (R-tipping). However, the potential implications of R-tipping in ecology remain understudied. We aim to facilitate the application of R-tipping theory in ecology with the objective of identifying which properties (e.g. level of organisation) increase susceptibility to rates of change. First, we clarify the fundamental difference between tipping caused by the magnitude as opposed to the rate of change crossing a threshold. Then we present examples of R-tipping from the ecological literature and seek the ecological properties related to higher sensitivity to rates of change. Specifically, we consider the role of the level of ecological organisation, spatial processes, eco-evolutionary dynamics and pair–wise interactions in mediating or buffering rate-induced transitions. Finally, we discuss how targeted experiments can investigate the mechanisms associated to increasing rates of change. Ultimately, we seek to highlight the need to better understand how rates of environmental change may induce ecological responses and to facilitate the systematic study of rates of environmental change in the context of current global change

A fast and sensitive method for the continuous in situ determination of dissolved methane and its d13C-isotope ratio in surface waters

A fast and sensitive method for the continuous determination of methane (CH4) and its stable carbon isotopic values (d13C-CH4) in surface waters was developed by applying a vacuum to a gas/liquid exchange membrane and measuring the extracted gases by a portable cavity ring-down spectroscopy analyser (M-CRDS). The M-CRDS was calibrated and characterized for CH4 concentration and d13C-CH4 with synthetic water standards. The detection limit of the M-CRDS for the simultaneous determination of CH4 and d13CCH4 is 3.6 nmol L21 CH4. A measurement precision of CH4 concentrations and d13C-CH4 in the range of 1.1%, respectively, 1.7& (1r) and accuracy (1.3%, respectively, 0.8& [1r]) was achieved for single measurements and averaging times of 10 min. The response time s of 5765 s allow determination of d13C-CH4 values more than twice as fast than other methods. The demonstrated M-CRDS method was applied and tested for Lake Stechlin (Germany) and compared with the headspace-gas chromatography and fast membrane CH4 concentration methods. Maximum CH4 concentrations (577 nmol L21) and lightest d13C-CH4 (235.2&) were found around the thermocline in depth profile measurements. The M-CRDS-method was in good agreement with other methods. Temporal variations in CH4 concentration and d13C-CH4 obtained in 24 h measurements indicate either local methane production/oxidation or physical variations in the thermocline. Therefore, these results illustrate the need of fast and sensitive analyses to achieve a better understanding of different mechanisms and pathways of CH4 formation in aquatic environments

Land-use type temporarily affects active pond community structure but not gene expression patterns

Changes in land use and agricultural intensification threaten biodiversity and ecosystem functioning of small water bodies. We studied 67 kettle holes (KH) in an agricultural landscape in northeastern Germany using landscape-scale metatranscriptomics to understand the responses of active bacterial, archaeal and eukaryotic communities to land-use type. These KH are proxies of the millions of small standing water bodies of glacial origin spread across the northern hemisphere. Like other landscapes in Europe, the study area has been used for intensive agriculture since the 1950s. In contrast to a parallel environmental DNA study that suggests the homogenization of biodiversity across KH, conceivably resulting from long-lasting intensive agriculture, land-use type affected the structure of the active KH communities during spring crop fertilization, but not a month later. This effect was more pronounced for eukaryotes than for bacteria. In contrast, gene expression patterns did not differ between months or across land-use types, suggesting a high degree of functional redundancy across the KH communities. Variability in gene expression was best explained by active bacterial and eukaryotic community structures, suggesting that these changes in functioning are primarily driven by interactions between organisms. Our results indicate that influences of the surrounding landscape result in temporary changes in the activity of different community members. Thus, even in KH where biodiversity has been homogenized, communities continue to respond to land management. This potential needs to be considered when developing sustainable management options for restoration purposes and for successful mitigation of further biodiversity loss in agricultural landscapes

Postglacial adaptations enabled colonization and quasi-clonal dispersal of ammonia-oxidizing archaea in modern European large lakes

Ammonia-oxidizing archaea (AOA) play a key role in the aquatic nitrogen cycle. Their genetic diversity is viewed as the outcome of evolutionary processes that shaped ancestral transition from terrestrial to marine habitats. However, current genome-wide insights into AOA evolution rarely consider brackish and freshwater representatives or provide their divergence timeline in lacustrine systems. An unbiased global assessment of lacustrine AOA diversity is critical for understanding their origins, dispersal mechanisms, and ecosystem roles. Here, we leveraged continental-scale metagenomics to document that AOA species diversity in freshwater systems is remarkably low compared to marine environments. We show that the uncultured freshwater AOA, "Candidatus Nitrosopumilus limneticus," is ubiquitous and genotypically static in various large European lakes where it evolved 13 million years ago. We find that extensive proteome remodeling was a key innovation for freshwater colonization of AOA. These findings reveal the genetic diversity and adaptive mechanisms of a keystone species that has survived clonally in lakes for millennia

Microbial and Chemical Characterization of Underwater Fresh Water Springs in the Dead Sea

Due to its extreme salinity and high Mg concentration the Dead Sea is characterized by a very low density of cells most of which are Archaea. We discovered several underwater fresh to brackish water springs in the Dead Sea harboring dense microbial communities. We provide the first characterization of these communities, discuss their possible origin, hydrochemical environment, energetic resources and the putative biogeochemical pathways they are mediating. Pyrosequencing of the 16S rRNA gene and community fingerprinting methods showed that the spring community originates from the Dead Sea sediments and not from the aquifer. Furthermore, it suggested that there is a dense Archaeal community in the shoreline pore water of the lake. Sequences of bacterial sulfate reducers, nitrifiers iron oxidizers and iron reducers were identified as well. Analysis of white and green biofilms suggested that sulfide oxidation through chemolitotrophy and phototrophy is highly significant. Hyperspectral analysis showed a tight association between abundant green sulfur bacteria and cyanobacteria in the green biofilms. Together, our findings show that the Dead Sea floor harbors diverse microbial communities, part of which is not known from other hypersaline environments. Analysis of the water’s chemistry shows evidence of microbial activity along the path and suggests that the springs supply nitrogen, phosphorus and organic matter to the microbial communities in the Dead Sea. The underwater springs are a newly recognized water source for the Dead Sea. Their input of microorganisms and nutrients needs to be considered in the assessment of possible impact of dilution events of the lake surface waters, such as those that will occur in the future due to the intended establishment of the Red Sea−Dead Sea water conduit

What makes a cyanobacterial bloom disappear? A review of the abiotic and biotic cyanobacterial bloom loss factors

Cyanobacterial blooms present substantial challenges to managers and threaten ecological and public health. Although the majority of cyanobacterial bloom research and management focuses on factors that control bloom initiation, duration, toxicity, and geographical extent, relatively little research focuses on the role of loss processes in blooms and how these processes are regulated. Here, we define a loss process in terms of population dynamics as any process that removes cells from a population, thereby decelerating or reducing the development and extent of blooms. We review abiotic (e.g., hydraulic flushing and oxidative stress/UV light) and biotic factors (e.g., allelopathic compounds, infections, grazing, and resting cells/programmed cell death) known to govern bloom loss. We found that the dominant loss processes depend on several system specific factors including cyanobacterial genera-specific traits, in situ physicochemical conditions, and the microbial, phytoplankton, and consumer community composition. We also address loss processes in the context of bloom management and discuss perspectives and challenges in predicting how a changing climate may directly and indirectly affect loss processes on blooms. A deeper understanding of bloom loss processes and their underlying mechanisms may help to mitigate the negative consequences of cyanobacterial blooms and improve current management strategies