Stable Carbon Isotope Signature of Methane Released From Phytoplankton

Unidad de excelencia María de Maeztu CEX2019-000940-MAquatic ecosystems play an important role in global methane cycling and many field studies have reported methane supersaturation in the oxic surface mixed layer (SML) of the ocean and in the epilimnion of lakes. The origin of methane formed under oxic condition is hotly debated and several pathways have recently been offered to explain the "methane paradox." In this context, stable isotope measurements have been applied to constrain methane sources in supersaturated oxygenated waters. Here we present stable carbon isotope signatures for six widespread marine phytoplankton species, three haptophyte algae and three cyanobacteria, incubated under laboratory conditions. The observed isotopic patterns implicate that methane formed by phytoplankton might be clearly distinguished from methane produced by methanogenic archaea. Comparing results from phytoplankton experiments with isotopic data from field measurements, suggests that algal and cyanobacterial populations may contribute substantially to methane formationobserved in the SML of oceans and lakes

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

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

The Bear Lake in Sovata: Fascinating haloclines, patterned biofilms

Heliotherme Salzwasserseen wie der Bärensee in Siebenbürgen haben eine stabile Dichteschichtung mit einer konzentrierten Salzlösung in der Tiefe und einer weniger salzhaltigen (und deshalb weniger dichten) Oberflächenschicht. Durch die Sonneneinstrahlung wird die Übergangsschicht (die Halokline) auf Temperaturen bis 40–45 °C aufgeheizt. Aufgrund der starken physikalisch-chemischen Gradienten existiert eine Reihe von biologischen Nischen. Mithilfe von Forschungstauchgängen wurde dieses einzigartige Ökosystem genauer untersucht. Besonders interessant sind die Biofilme von Cyanobakterien, die einen komplexen Jahreszyklus mit der Bildung von Netzmustern im Spätherbst zeigen sowie das Vorhandensein roter Fe2O3- haltigen Flecken auf dem Schlamm, die wahrscheinlich aus dem schwarzen FeS-haltigen Schlamm durch eisenoxidierende Bakterien gebildet werden. In den Biofilmen wurden auch Kieselalgentaxa gefunden, deren Verwandte aus salinen Habitaten bekannt sind.Heliothermic lakes, like the Bear Lake in Transylvania, have a stable stratification with a concentrated saline layer at the bottom and a less saline (thus lower density) surface layer. Due to solar radiation, the transition layer (the halocline) is heated up to 40–45 °C. The pronounced physico-chemical gradients result in a series of biological niches. Scientific diving was used to investigate this unique ecosystem. Biofilms of cyanobacteria are especially interesting. They follow a complex annual cycle by forming reticulated patterns in late autumn presenting characteristic red Fe2O3 spots on the mud, probably formed from the black FeS-containing mud by iron-oxidizing bacteria. Diatom taxa, whose relatives are known for inhabiting saline habitats, have also been found in the biofilms

Heterozygous, Polyploid, Giant Bacterium, Achromatium, Possesses an Identical Functional Inventory Worldwide across Drastically Different Ecosystems

Achromatium is large, hyperpolyploid and the only known heterozygous bacterium. Single cells contain approximately 300 different chromosomes with allelic diversity far exceeding that typically harbored by single bacteria genera. Surveying all publicly available sediment sequence archives, we show that Achromatium is common worldwide, spanning temperature, salinity, pH, and depth ranges normally resulting in bacterial speciation. Although saline and freshwater Achromatium spp. appear phylogenetically separated, the genus Achromatium contains a globally identical, complete functional inventory regardless of habitat. Achromatium spp. cells from differing ecosystems (e.g., from freshwater to saline) are, unexpectedly, equally functionally equipped but differ in gene expression patterns by transcribing only relevant genes. We suggest that environmental adaptation occurs by increasing the copy number of relevant genes across the cell’s hundreds of chromosomes, without losing irrelevant ones, thus maintaining the ability to survive in any ecosystem type. The functional versatility of Achromatium and its genomic features reveal alternative genetic and evolutionary mechanisms, expanding our understanding of the role and evolution of polyploidy in bacteria while challenging the bacterial species concept and drivers of bacterial speciation

Diversity of Iron Oxidizing and Reducing Bacteria in Flow Reactors in the Äspö Hard Rock Laboratory

Processes of iron mineralization are of great significance to the understanding of Early-Earth geochemistry. Of specific interest are processes at circumneutral pH, where chemical oxidation of Fe can outcompete biological oxidation. To better understand microbially-induced mineral formation and the composition of the involved microbial communities, we set up a series of flow-reactors in the Äspö Hard Rock Laboratory, a 3.6 km tunnel that runs under the Baltic Sea. Various aquifers of Fe2+-rich brackish to saline waters penetrate the tunnel through a series of fractions. The reactors were set up with different combinations of light and aeration conditions, and were connected to three aquifers of differing chemical composition and age. Using a combination of 454 pyrosequencing and CAtalyzed Reporter Deposition Fluorescent In Situ Hybridization we analyzed the bacterial community from these reactors in two consecutive seasons half a year apart. A general decrease in diversity was observed towards the deep part of the tunnel. Multivariate modeling of the community composition and environmental parameters shows that the overall diversity of the microbial community is controlled by salinity as well as carbon and nitrogen sources. However, the composition of iron oxidizing bacteria is driven by pH, O2 and the availability of Fe2+. The latter is mostly supplied by Fe3+ reduction in the reactors. Thus the reactors form a self-sustained ecosystem. Several genera of known aerobic and anaerobic iron oxidizing bacteria were found. Mariprofundus sp. was found to be dominant in many of the samples. This is the first detection of this marine species in groundwater. The microbial community in the reactors is unique in each site, while that in the exposed tunnel is more homogenous. Therefore we suggest that the flow reactors are a good model system to study the nonaccessible microbial communities that are likely present in cracks and crevices of the surrounding bedrock

Reply to ‘Oxic methanogenesis is only a minor source of lake-wide diffusive CH₄emissions from lakes’

The prevailing paradigm in methane research is that biological methane production is exclusive to anoxic or near-anoxic habitats such as sediments and oxygen-deficient bottom waters in lakes. Paradoxically, methane supersaturation in oxic lake waters is widely reported. To resolve this paradox while preserving the paradigm, some researchers assume this methane originates entirely from anoxic sources and is then transported to the oxic waters through physical processes1,2,3. However, multiple recent studies have repeatedly shown, methane production can and does occur under oxic conditions on land, in the seas and in freshwaters, driven by diverse organisms within different life domains (Table 1 and references therein) and via photochemical conversion4. These findings raise legitimate questions about the nature of the environmental dynamics and global budget of methane. Because oxic methane production (OMP) is a recent discovery, its contribution to atmospheric emission is unknown. We conducted a whole-lake basin methane mass balance and analysed relevant literature data to estimate the contribution of OMP to surface emission versus lake morphometry.</p

A novel method to sample individual marine snow particles for downstream molecular analyses

Abstract The ocean–atmosphere exchange of carbon largely depends on the balance between carbon export of particulate organic carbon (POC) as sinking marine particles, and POC remineralization by attached microbial communities. Despite the vast spectrum of types, sources, ages, shapes, and composition of individual sinking particles, they are usually considered as a bulk together with their associated microbial communities. This limits our mechanistic understanding of the biological carbon pump (BCP) and its feedback on the global carbon cycle. We established a method to sample individual particles while preserving their shape, structure, and nucleic acids by placing a jellified RNA‐fixative at the bottom of drifting sediment traps. Coupling imaging of individual particles with associated 16S rRNA analysis reveals that active bacterial communities are highly heterogenous from one particles origin to another. In contrast to lab‐made particles, we found that complex in situ conditions lead to heterogeneity even within the same particle type. Our new method allows to associate patterns of active prokaryotic and functional diversity to particle features, enabling the detection of potential remineralization niches. This new approach will therefore improve our understanding of the BCP and numerical representation in the context of a rapidly changing ocean

Potential for Natural Attenuation of Domestic and Agricultural Pollution in Karst Groundwater Environments

In karst areas, anthropogenic contaminants reach the subsurface with detrimental effects on the groundwater ecosystem and downstream springs, which often serve as drinking water sources for the local human communities. We analyzed the water chemistry and microbial community composition in upstream and downstream locations of five hydrokarst systems (HKS) during four seasons. Conductivity and nitrates were higher in the downstream springs than in the pre-karst waters, whereas the concentration of organic matter, considered here as a pollution indicator, was lower. The microbial community composition varied largely between upstream and downstream locations, with multiple species of potentially pathogenic bacteria decreasing in the HKS. Bacteria indicative of pollution decreased as well when passing through the HKS, but potential biodegraders increased. This suggests that the HKS can filter out part of the polluting organic matter and, with it, part of the associated microorganisms. Nevertheless, the water quality, including the presence of pathogens in downstream springs, must be further monitored to control whether the water is appropriate for consumption. In parallel, the human populations located upstream must be advised of the risks resulting from their daily activities, improper stocking of their various wastes and dumping of their refuse in surface streams

From microbes to mammals: agriculture homogenizes pond biodiversity across different land-use types

The diversity and composition of biological communities in ecosystems is typically linked to land use. Consequently, intensive agriculture has a strong influence on these patterns, including a reduction and homogenization of species diversity. Kettle holes (KH; also known as potholes) are small water bodies (300 million reads, were analyzed with phyloFlash and Kraken2 using the SILVA_SSU_Ref database. Subsequently, the sequences were grouped based on taxonomy. The use of different annotation pipelines resulted in similar patterns. A subset of the data was analyzed using DADA2, generating amplicon sequence variants. Clustering the sequences as variants or according to taxonomy resulted in identical patterns, suggesting that broad taxonomical groupings provide sufficient resolution for general overviews.Annotation of the eukaryotic community was challenging, as none of the currently available databases contains sufficient high-quality sequences to cover the entire phylogenetic breadth. To overcome this limitation, we used the SILVA_SSU_Parc database, which also contains short sequences excluded from SILVA_SSU_Ref, thus extending the taxonomic base of the analysis. The curated, high-quality PR2 eukaryotic database did not provide better results than the SILVA_SSU_Ref database. An incompatibility between the SILVA and classical taxonomic nomenclature resulted in a ‘language barrier,’ which could be partly resolved by using the parallel EMBL taxonomy provided in the SILVA databases. Nevertheless, we propose that short-read SSU-based eukaryotic taxonomic annotations should be validated by other means.Despite such methodological limitations, our study demonstrates that deep amplicon sequencing of eDNA return a reliable picture of the biodiversity in complex ecosystems. Such information is sufficient to identify biodiversity patterns across the three domains of life and can serve to pinpoint taxonomic groups which should be investigated by a more detailed approach.Our study concluded that long-term exposure to intensive agriculture results in biodiversity homogenization across diverse taxonomic groups, removing most differences in biodiversity patterns among land-use types. This outcome contrasts with biodiversity patterns associated with sediments of the KH, where temporal coverage by the eDNA analyses extends back to at least the onset of intensive agriculture. However, metatranscriptomic analyses, reflecting the distribution of activities rather than relative abundance, revealed temporal differences in the structure of the active community in KH of the investigated land-use types, matching times of field fertilization. Thus, even in a landscape where biodiversity has been homogenized, inputs from the surroundings result in short-term activity changes of different organisms. This needs to be considered when developing new management schemes needed to counteract the current biodiversity loss