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Quantifying fair national shares of the remaining global carbon budget has proven challenging. Here, we propose an indicator-additional carbon accountability-that quantifies countries' responsibility for mitigation and CO 2 removal in addition to achieving their own targets. Considering carbon debts since 1990 and future claims based on countries' emission pathways, the indicator uses an equal cumulative per capita emissions approach to allocate accountability for closing the mitigation gap among countries with a positive total excessive carbon claim. The carbon budget is exceeded by 576 Gigatonnes of fossil CO 2 when limiting warming below 1.5 °C (50% probability). Additional carbon accountability is highest for the United States and China, and highest per capita for the United Arab Emirates and Russia. Assumptions on carbon debts strongly impact the results for most countries. The ability to pay for this accountability is challenging for Iran, Kazakhstan and several BRICS+ members, in contrast to the G7 members., (© 2024. The Author(s).)

This planetary boundaries framework update finds that six of the nine boundaries are transgressed, suggesting that Earth is now well outside of the safe operating space for humanity. Ocean acidification is close to being breached, while aerosol loading regionally exceeds the boundary. Stratospheric ozone levels have slightly recovered. The transgression level has increased for all boundaries earlier identified as overstepped. As primary production drives Earth system biosphere functions, human appropriation of net primary production is proposed as a control variable for functional biosphere integrity. This boundary is also transgressed. Earth system modeling of different levels of the transgression of the climate and land system change boundaries illustrates that these anthropogenic impacts on Earth system must be considered in a systemic context.

Climate tipping points occur when change in a part of the climate system becomes self-perpetuating beyond a warming threshold, leading to substantial Earth system impacts. Synthesizing paleoclimate, observational, and model-based studies, we provide a revised shortlist of global "core" tipping elements and regional "impact" tipping elements and their temperature thresholds. Current global warming of ~1.1°C above preindustrial temperatures already lies within the lower end of some tipping point uncertainty ranges. Several tipping points may be triggered in the Paris Agreement range of 1.5 to <2°C global warming, with many more likely at the 2 to 3°C of warming expected on current policy trajectories. This strengthens the evidence base for urgent action to mitigate climate change and to develop improved tipping point risk assessment, early warning capability, and adaptation strategies.

Forest and savanna ecosystems naturally exist as alternative stable states. The maximum capacity of these ecosystems to absorb perturbations without transitioning to the other alternative stable state is referred to as 'resilience'. Previous studies have determined the resilience of terrestrial ecosystems to hydroclimatic changes predominantly based on space-for-time substitution. This substitution assumes that the contemporary spatial frequency distribution of ecosystems' tree cover structure holds across time. However, this assumption is problematic since ecosystem adaptation over time is ignored. Here we empirically study tropical forests' stability and hydroclimatic adaptation dynamics by examining remotely sensed tree cover change (ΔTC; aboveground ecosystem structural change) and root zone storage capacity (S r ; buffer capacity towards water-stress) over the last two decades. We find that ecosystems at high (>75%) and low (<10%) tree cover adapt by instigating considerable subsoil investment, and therefore experience limited ΔTC-signifying stability. In contrast, unstable ecosystems at intermediate (30%-60%) tree cover are unable to exploit the same level of adaptation as stable ecosystems, thus showing considerable ΔTC. Ignoring this adaptive mechanism can underestimate the resilience of the forest ecosystems, which we find is largely underestimated in the case of the Congo rainforests. The results from this study emphasise the importance of the ecosystem's temporal dynamics and adaptation in inferring and assessing the risk of forest-savannah transitions under rapid hydroclimatic change., (© 2022 The Authors. Global Change Biology published by John Wiley & Sons Ltd.)

Heatwaves are extreme weather events that have become more frequent and intense in Europe over the past decades. Heatwaves are often coupled to droughts. The combination of them lead to severe ecological and socio-economic impacts. Heatwaves can self-amplify through internal climatic feedback that reduces local precipitation. Understanding the terrestrial sources of local precipitation during heatwaves might help identify mitigation strategies on land management and change that alleviate impacts. Moisture recycling of local water sources through evaporation allows a region to maintain precipitation in the same region or, by being transported by winds, in adjacent regions. To understand the role of terrestrial moisture sources for sustaining precipitation during heatwaves, we backtrack and analyse the precipitation sources of Northern, Western, and Southern sub-regions across Europe during 20 heatwave periods between 1979 and 2018 using the moisture tracking model Water Accounting Model-2layers (WAM-2layers). In Northern and Western Europe, we find that stabilizing anticyclonic patterns reduce the climatological westerly supply of moisture, mainly from the North Atlantic Ocean, and enhances the moisture flow from the eastern Euro-Asian continent and from within their own regions-suggesting over 10% shift of moisture supply from oceanic to terrestrial sources. In Southern Europe, limited local moisture sources result in a dramatic decrease in the local moisture recycling rate. Forests uniformly supply additional moisture to all regions during heatwaves and thus contribute to buffer local impacts. This study suggests that terrestrial moisture sources, especially forests, may potentially be important to mitigate moisture scarcity during heatwaves in Europe., Supplementary Information: The online version contains supplementary material available at 10.1007/s00382-021-05921-7., Competing Interests: Conflict of interestThe authors have no conflicts of interest to disclose., (© The Author(s) 2021.)

Tropical forests modify the conditions they depend on through feedbacks at different spatial scales. These feedbacks shape the hysteresis (history-dependence) of tropical forests, thus controlling their resilience to deforestation and response to climate change. Here, we determine the emergent hysteresis from local-scale tipping points and regional-scale forest-rainfall feedbacks across the tropics under the recent climate and a severe climate-change scenario. By integrating remote sensing, a global hydrological model, and detailed atmospheric moisture tracking simulations, we find that forest-rainfall feedback expands the geographic range of possible forest distributions, especially in the Amazon. The Amazon forest could partially recover from complete deforestation, but may lose that resilience later this century. The Congo forest currently lacks resilience, but is predicted to gain it under climate change, whereas forests in Australasia are resilient under both current and future climates. Our results show how tropical forests shape their own distributions and create the climatic conditions that enable them.

Climate change is expected to increase the incidences of extremes in environmental conditions. To investigate how repeated disturbances affect microbial ecosystem resistance, natural lake bacterioplankton communities were subjected to repeated temperature disturbances of two intensities (25 °C and 35 °C), and subsequently to an acidification event. We measured functional parameters (bacterial production, abundance, extracellular enzyme activities) and community composition parameters (richness, evenness, niche width) and found that, compared to undisturbed control communities, the 35 °C treatment was strongly affected in all parameters, while the 25 °C treatment did not significantly differ from the control. Interestingly, exposure to multiple temperature disturbances caused gradually increasing stability in the 35 °C treatment in some parameters, while others parameters showed the opposite, indicating that the choice of parameters can strongly affect the outcome of a study. The acidification event did not lead to stronger changes in community structure, but functional resistance of bacterial production towards acidification in the 35 °C treatments increased. This indicates that functional resistance in response to a novel disturbance can be increased by previous exposure to another disturbance, suggesting similarity in stress tolerance mechanisms for both disturbances. These results highlight the need for understanding function- and disturbance-specific responses, since general responses are likely to be unpredictable.

The planetary boundaries framework defines the "safe operating space for humanity" represented by nine global processes that can destabilize the Earth System if perturbed. The water planetary boundary attempts to provide a global limit to anthropogenic water cycle modifications, but it has been challenging to translate and apply it to the regional and local scales at which water problems and management typically occur. We develop a cross-scale approach by which the water planetary boundary could guide sustainable water management and governance at subglobal contexts defined by physical features (e.g., watershed or aquifer), political borders (e.g., city, nation, or group of nations), or commercial entities (e.g., corporation, trade group, or financial institution). The application of the water planetary boundary at these subglobal contexts occurs via two approaches: (i) calculating fair shares , in which local water cycle modifications are compared to that context's allocation of the global safe operating space, taking into account biophysical, socioeconomic, and ethical considerations; and (ii) defining a local safe operating space, in which interactions between water stores and Earth System components are used to define local boundaries required for sustaining the local water system in stable conditions, which we demonstrate with a case study of the Cienaga Grande de Santa Marta wetlands in Colombia. By harmonizing these two approaches, the water planetary boundary can ensure that water cycle modifications remain within both local and global boundaries and complement existing water management and governance approaches., (©2020 The Authors.)

Natural microbial communities in soils are highly diverse, allowing for rich networks of microbial interactions to unfold. Identifying key players in these networks is difficult as the distribution of microbial diversity at the local scale is typically non-uniform, and is the outcome of both abiotic environmental factors and microbial interactions. Here, using spatially resolved microbial presence-absence data along an aquifer transect contaminated with hydrocarbons, we combined co-occurrence analysis with association rule mining to identify potential keystone species along the hydrocarbon degradation process. Derived co-occurrence networks were found to be of a modular structure, with modules being associated with specific spatial locations and metabolic activity along the contamination plume. Association rules identify species that never occur without another, hence identifying potential one-sided cross-feeding relationships. We find that hub nodes in the rule network appearing in many rules as targets qualify as potential keystone species that catalyze critical transformation steps and are able to interact with varying partners. By contrasting analysis based on data derived from bulk samples and individual soil particles, we highlight the importance of spatial sample resolution. While individual inferred interactions are hypothetical in nature, requiring experimental verification, the observed global network patterns provide a unique first glimpse at the complex interaction networks at work in the microbial world., Competing Interests: The authors declare no conflict of interest.

Water security is key to planetary resilience for human society to flourish in the face of global change. Atmospheric moisture recycling - the process of water evaporating from land, flowing through the atmosphere, and falling out again as precipitation over land - is the invisible mechanism by which water influences resilience, that is the capacity to persist, adapt, and transform. Through land-use change, mainly by agricultural expansion, humans are destabilizing and modifying moisture recycling and precipitation patterns across the world. Here, we provide an overview of how moisture recycling changes may threaten tropical forests, dryland ecosystems, agriculture production, river flows, and water supplies in megacities, and review the budding literature that explores possibilities to more consciously manage and govern moisture recycling. Novel concepts such as the precipitationshed allows for the source region of precipitation to be understood, addressed and incorporated in existing water resources tools and sustainability frameworks. We conclude that achieving water security and resilience requires that we understand the implications of human influence on moisture recycling, and that new research is paving the way for future possibilities to manage and mitigate potentially catastrophic effects of land use and water system change., (© 2019 The Authors.)

Projections of global warming in Africa are generally associated with increasing aridity and decreasing water availability. However, most freshwater assessments focus on single hydroclimatic indicators (e.g., runoff, precipitation, or aridity), lacking analysis on combined changes in evaporative demand, and water availability on land. There remains a high degree of uncertainty over water implications at the basin scale, in particular for the most water-consuming sector-food production. Using the Budyko framework, we perform an assessment of future hydroclimatic change for the 50 largest African basins, finding a consistent pattern of change in four distinct regions across the two main emission scenarios corresponding to the Paris Agreement, and the business as usual. Although the Paris Agreement is likely to lead to less intense changes when compared to the business as usual, both scenarios show the same pattern of hydroclimatic shifts, suggesting a potential roadmap for hydroclimatic adaptation. We discuss the social-ecological implications of the projected hydroclimatic shifts in the four regions and argue that climate policies need to be complemented by soil and water conservation practices to make the best use of future water resources., (©2019. The Authors.)

We explore the risk that self-reinforcing feedbacks could push the Earth System toward a planetary threshold that, if crossed, could prevent stabilization of the climate at intermediate temperature rises and cause continued warming on a "Hothouse Earth" pathway even as human emissions are reduced. Crossing the threshold would lead to a much higher global average temperature than any interglacial in the past 1.2 million years and to sea levels significantly higher than at any time in the Holocene. We examine the evidence that such a threshold might exist and where it might be. If the threshold is crossed, the resulting trajectory would likely cause serious disruptions to ecosystems, society, and economies. Collective human action is required to steer the Earth System away from a potential threshold and stabilize it in a habitable interglacial-like state. Such action entails stewardship of the entire Earth System-biosphere, climate, and societies-and could include decarbonization of the global economy, enhancement of biosphere carbon sinks, behavioral changes, technological innovations, new governance arrangements, and transformed social values., Competing Interests: The authors declare no conflict of interest., (Copyright © 2018 the Author(s). Published by PNAS.)

Most natural environments are characterized by frequent changes of their abiotic conditions. Microorganisms can respond to such changes by switching their physiological state between activity and dormancy allowing them to endure periods of unfavorable abiotic conditions. As a consequence, the competitiveness of microbial species is not simply determined by their growth performance under favorable conditions but also by their ability and readiness to respond to periods of unfavorable environmental conditions. The present study investigates the relevance of factors controlling the abundance and activity of individual bacterial species competing for an intermittently supplied substrate. For this purpose, numerical experiments were performed addressing the response of microbial systems to regularly applied feeding pulses. Simulation results show that community dynamics may exhibit a non-trivial link to the frequency of the external constraints and that for a certain combination of these environmental conditions coexistence of species is possible. The ecological implication of our results is that even non-dominant, neglected species can have a strong influence on realized species composition of dominant key species, due to their invisible presence enable the coexistence between important key species and by this affecting provided function of the system., (© FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Loading of water bodies with dissolved organic carbon (DOC) and dissolved total nitrogen (DTN) affects their integrity and functioning. Microbial interactions mitigate the negative effects of high nutrient loads in these ecosystems. Despite numerous studies on how biodiversity mediates ecosystem functions, whether and how diversity and complexity of microbial food webs (horizontal, vertical) and the underlying ecological mechanisms influence nutrient removal has barely been investigated. Using microbial microcosms accommodating systematic combinations of prey (bacteria) and predator (protists) species, we showed that increasing bacterial richness improved the extent and reliability of DOC and DTN removal. Bacterial diversity drove nutrient removal either due to species foraging physiology or functional redundancy, whereas protistan diversity affected nutrient removal through bacterial prey resource partitioning and changing nutrient balance in the system. Our results demonstrate that prey-predator diversity and trophic interactions interactively determine nutrient contents, thus implying the vital role of microbial trophic complexity as a biological buffer against DOC and DTN., (© 2016 The Author(s).)

In this study, we investigated the effect of land use intensity, soil parameters and vegetation on protistan communities in grassland soils. We performed qualitative (T-RFLP) and quantitative (qPCR) analyses using primers specifically targeting the 18S rRNA gene for all Eukarya and for two common flagellate groups, i.e. the Chrysophyceae and the Kinetoplastea. Both approaches were applied to extracted soil DNA and RNA, in order to distinguish between the potentially active protists (i.e. RNA pool) and the total protistan communities, including potentially inactive and encysted cells (i.e. DNA pool). Several environmental determinants such as site, soil parameters and vegetation had an impact on the T-RFLP community profiles and the abundance of the quantified 18S rRNA genes. Correlating factors often differed between quantitative (qPCR) and qualitative (T-RFLP) approaches. For instance the Chrysophyceae/Eukarya 18S rDNA ratio as determined by qPCR correlated with the C/N ratio, whereas the community composition based on T-RLFP analysis was not affected indicating that both methods taken together provide a more complete picture of the parameters driving protist diversity. Moreover, distinct T-RFs were obtained, which could serve as potential indicators for either active organisms or environmental conditions like water content. While site was the main determinant across all investigated exploratories, land use seemed to be of minor importance for structuring protist communities. The impact of other parameters differed between the target groups, e.g. Kinetoplastea reacted on changes to water content on all sites, whereas Chrysophyceae were only affected in the Schorfheide. Finally, in most cases different responses were observed on RNA- and DNA-level, respectively. Vegetation for instance influenced the two flagellate groups only at the DNA-level across all sites. Future studies should thus include different protistan groups and also distinguish between active and inactive cells, in order to reveal causal shifts in community composition and abundance in agriculturally used systems., (Copyright © 2015. Published by Elsevier B.V.)

Assessing the ecological impacts of environmental change requires knowledge of the relationship between biodiversity and ecosystem functioning. The exact nature of this relationship can differ considerably between ecosystems, with consequences for the efficacy of species diversity as a buffer against environmental change. Using a microbial model system, we show that the relationship can vary depending on environmental conditions. Shapes suggesting functional redundancy in one environment can change, suggesting functional differences in another environment. We find that this change is due to shifting species roles and interactions. Species that are functionally redundant in one environment may become pivotal in another. Thus, caution is advised in drawing conclusions about functional redundancy based on a single environmental situation. It also implies that species richness is important because it provides a pool of species with potentially relevant traits. These species may turn out to be essential performers or partners in new interspecific interactions after environmental change. Therefore, our results challenge the generality of functional redundancy.

Biogas is an important renewable energy carrier. It is a product of stepwise anaerobic degradation of organic materials by highly diverse microbial communities forming complex interlinking metabolic networks. Knowledge about the microbial background of long-term stable process performance in full-scale reactors is crucial for rationally improving the efficiency and reliability of biogas plants. To generate such knowledge, in the present study three parallel mesophilic full-scale reactors fed exclusively with energy crops were sampled weekly over one year. Physicochemical process parameters were determined and the microbial communities were analysed by terminal restriction fragment length polymorphism (T-RFLP) fingerprinting and 454-amplicon sequencing. For investigating the methanogenic community, a high-resolution T-RFLP approach based on the mcrA gene was developed by selecting restriction enzymes with improved taxonomic resolution compared to previous studies. Interestingly, no Methanosarcina-related generalists, but rather specialized hydrogenotrophic and acetoclastic methanogenic taxa were detected. In general, the microbial communities in the non-connected reactors were remarkably stable and highly similar indicating that identical environmental and process parameters resulted in identical microbial assemblages and dynamics. Practical implications such as flexible operation schemes comprising controlled variations of process parameters for an efficient microbial resource management under fluctuating process conditions are discussed., (© FEMS 2015. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.)

The planetary boundaries framework defines a safe operating space for humanity based on the intrinsic biophysical processes that regulate the stability of the Earth system. Here, we revise and update the planetary boundary framework, with a focus on the underpinning biophysical science, based on targeted input from expert research communities and on more general scientific advances over the past 5 years. Several of the boundaries now have a two-tier approach, reflecting the importance of cross-scale interactions and the regional-level heterogeneity of the processes that underpin the boundaries. Two core boundaries—climate change and biosphere integrity—have been identified, each of which has the potential on its own to drive the Earth system into a new state should they be substantially and persistently transgressed., (Copyright © 2015, American Association for the Advancement of Science.)

Knowledge of metabolic processes is collected in easily accessable online databases which are increasing rapidly in content and detail. Using these databases for the automatic construction of metabolic network models requires high accuracy and consistency. In this bipartite study we evaluate current accuracy and consistency problems using the KEGG database as a prominent example and propose design principles for dealing with such problems. In the first half, we present our computational approach for classifying inconsistencies and provide an overview of the classes of inconsistencies we identified. We detected inconsistencies both for database entries referring to substances and entries referring to reactions. In the second part, we present strategies to deal with the detected problem classes. We especially propose a rule-based database approach which allows for the inclusion of parameterised molecular species and parameterised reactions. Detailed case-studies and a comparison of explicit networks from KEGG with their anticipated rule-based representation underline the applicability and scalability of this approach.

Serial repitching of brewing yeast inoculates is an important economic factor in the brewing industry, as their propagation is time and resource intensive. Here, we investigated whether replicative aging and/or the population distribution status changed during serial repitching in three different breweries with the same brewing yeast strain but different abiotic backgrounds and repitching regimes with varying numbers of reuses. Next to bud scar numbers the DNA content of the Saccharomyces pastorianus HEBRU cells was analyzed. Gene expression patterns were investigated using low-density microarrays with genes for aging, stress, storage compound metabolism and cell cycle. Two breweries showed a stable rejuvenation rate during serial repitching. In a third brewery the fraction of virgin cells varied, which could be explained with differing wort aeration rates. Furthermore, the number of bud scars per cell and cell size correlated in all 3 breweries throughout all runs. Transcriptome analyses revealed that from the 6th run on, mainly for the cells positive gene expression could be seen, for example up-regulation of trehalose and glycogen metabolism genes. Additionally, the cells' settling in the cone was dependent on cell size, with the lowest and the uppermost cone layers showing the highest amount of dead cells. In general, cells do not progressively age during extended serial repitching., (Copyright © 2014 Elsevier B.V. All rights reserved.)

Qualitative and quantitative 16S rRNA gene-based real-time PCR and direct sequencing were applied for rapid detection and identification of bacterial DNA (bactDNA) in 356 ascites samples. bactDNA was detected in 35% of samples, with a mean of 3.24 log copies ml(-1). Direct sequencing of PCR products revealed 62% mixed chromatograms predominantly belonging to Gram-positive bacteria. Terminal restriction fragment length polymorphism (T-RFLP) results of a sample subset confirmed sequence data showing polymicrobial DNA contents in 67% of bactDNA-positive ascites samples.

Bottom-fermenting Saccharomyces pastorianus strains driving brewing fermentation processes are usually reused several times. It is still unclear, whether the number of successions may have an impact on cell physiology prompting consequences for brewing quality. In this study, fermentation performance of up to twenty consecutive runs in a brewery was investigated. For each run mRNA expression levels of cellular marker molecules, which are known to correlate with metabolism, hexose transport, aging processes, stress response mechanisms and flocculation capability was estimated to obtain information on changes in cell physiology over the successive runs. Low-density microarrays were used for this purpose and the resulting gene expression profiles were finally correlated with changes in the abiotic micro-environments. A surprising stability of the marker molecule expression profiles within each specific serial repitching was stated. Loss of flocculation or an advanced aging could not be detected during serial repitching in the analyzed brewery. However, certain runs of the serial repitchings showed high variation in stress response which was found to be caused by perturbations of the abiotic conditions. Regardless, the study showed that S. pastorianus can be used repeatedly in serial repitching processes without loss of prominent physiological characteristics., (Copyright © 2013 Elsevier B.V. All rights reserved.)

Predation influences prey diversity and productivity while it effectuates the flux and reallocation of organic nutrients into biomass at higher trophic levels. However, it is unknown how bacterivorous protists are influenced by the diversity of their bacterial prey. Using 456 microcosms, in which different bacterial mixtures with equal initial cell numbers were exposed to single or multiple predators (Tetrahymena sp., Poterioochromonas sp. and Acanthamoeba sp.), we showed that increasing prey richness enhanced production of single predators. The extent of the response depended, however, on predator identity. Bacterial prey richness had a stabilizing effect on predator performance in that it reduced variability in predator production. Further, prey richness tended to enhance predator evenness in the predation experiment including all three protists predators (multiple predation experiment). However, we also observed a negative relationship between prey richness and predator production in multiple predation experiments. Mathematical analysis of potential ecological mechanisms of positive predator diversity-functioning relationships revealed predator complementarity as a factor responsible for both enhanced predator production and prey reduction. We suggest that the diversity at both trophic levels interactively determines protistan performance and might have implications in microbial ecosystem processes and services.

Micro-organisms are known to degrade a wide range of toxic substances. How the environment shapes microbial communities in polluted ecosystems and thus influences degradation capabilities is not yet fully understood. In this study, we investigated microbial communities in a highly complex environment: the capillary fringe and subjacent sediments in a hydrocarbon-contaminated aquifer. Sixty sediment sections were analysed using terminal restriction fragment length polymorphism (T-RFLP) fingerprinting, cloning and sequencing of bacterial and archaeal 16S rRNA genes, complemented by chemical analyses of petroleum hydrocarbons, methane, oxygen and alternative terminal electron acceptors. Multivariate statistics revealed concentrations of contaminants and the position of the water table as significant factors shaping the microbial community composition. Micro-organisms with highest T-RFLP abundances were related to sulphate reducers belonging to the genus Desulfosporosinus, fermenting bacteria of the genera Sedimentibacter and Smithella, and aerobic hydrocarbon degraders of the genus Acidovorax. Furthermore, the acetoclastic methanogens Methanosaeta, and hydrogenotrophic methanogens Methanocella and Methanoregula were detected. Whereas sulphate and sulphate reducers prevail at the contamination source, the detection of methane, fermenting bacteria and methanogenic archaea further downstream points towards syntrophic hydrocarbon degradation., (© 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.)

Altering environmental conditions change structures of microbial communities. These effects have an impact on the single-cell level and can be sensitively detected using community flow cytometry. However, although highly accurate, microbial monitoring campaigns are still rarely performed applying this technique. One reason is the limited access to pattern analysis approaches for the evaluation of microbial cytometric data. In this article, a new analyzing tool, Cytometric Histogram Image Comparison (CHIC), is presented, which realizes trend interpretation of variations in microbial community structures (i) without any previous definition of gates, by working (ii) person independent, and (iii) with low computational demand. Various factors influencing a sensitive determination of changes in community structures were tested. The sensitivity of this technique was found to discriminate down to 0.5% internal variation. The final protocol was exemplarily applied to a complex microbial community dataset, and correlations to experimental variation were successfully shown., (Copyright © 2013 International Society for Advancement of Cytometry.)

Cytometric monitoring of microbial community dynamics can be used to estimate stability of technical microbial processes like biogas production by analysis of segregated cell abundance changes. In this study, structure variations of a biogas community were cytometrically recorded over 9 months and found to be of diagnostic value for process details. The reactor regime was intentionally disturbed with regard to substrate overload or H(2)S accumulation. A single-cell based approach called cytometric bar coding (CyBar) for fast identification of reactive subcommunities was used. Functionality of specific subcommunities was uncovered by processing CyBar data with abiotic reactor parameters using Spearman's correlation coefficient. Twenty subcommunities showed a discrete and divergent behavior. For example, a 4-fold substrate overload increased the cell number of two acidogenic index subcommunities to 176 and 193% within three days. Supplementary analyses were done using DNA fingerprinting, cloning, and sequencing. Bioreactor perturbations were shown to create cell abundance changes in subcommunities rather than variations in their phylogenetic composition. The used workflow and macros are ready-to-use tools and allow on-site monitoring and interpretation of variation in microbial community functions within a few hours.

Plant growth is an important process in physiological as well as ecological respect and a number of metabolic parameters (elemental ratios as well as steady-state levels of individual metabolites) have been demonstrated to reflect this process on the whole plant level. Since plant growth is highly localized and is the result of a complex interplay of metabolic activities in sink and source organs, we propose that ratios in metabolite levels of sink and source organs are particularly well suited to characterize this process. To demonstrate such a connection, we studied organ-specific metabolite ratios from Lotus japonicus treated with mineral nutrients, salt stress or arbuscular mycorrhizal fungi. The plants were displaying a wide range of biomass and of flower/biomass ratios. In the analysis of our data we looked for correlations between shifts in sink/source metabolite ratios and plant productivity (biomass accumulated at the time of harvest). In addition we correlated shifts in metabolite ratios comparing competing generative and vegetative sink organs with shifts in productivity of the two organs (changes in flower/biomass ratios). In our analyses we observed clear shifts of carbohydrates and of compounds connected to nitrogen metabolism in favour of sink organs of particularly high productivity. These shifts were in agreement with general differences in metabolite steady-state levels when comparing sink and source organs. Our findings suggest that differentiation of sink and source organs during sampling for metabolomic experiments substantially increases the amount of information obtained from such experiments.

Alkanes are major constituents of plant-derived waxy materials. In this study, we investigated the abundance, community structure and activity of bacteria harbouring the alkane monooxygenase gene alkB, which catalyses a major step in the pathway of aerobic alkane degradation in the litter layer, the litter-soil interface and in bulk soil at three time points during the degradation of maize and pea plant litter (2, 8 and 30 weeks) to improve our understanding about drivers for microbial performance in different soil compartments. Soil cores of different soil textures (sandy and silty) were taken from an agricultural field and incubated at constant laboratory conditions. The abundance of alkB genes and transcripts (by qPCR) as well as the community structure (by terminal restriction fragment polymorphism fingerprinting) were measured in combination with the concentrations and composition of alkanes. The results obtained indicate a clear response pattern of all investigated biotic and abiotic parameters depending on the applied litter material, the type of soil used, the time point of sampling and the soil compartment studied. As expected the distribution of alkanes of different chain length formed a steep gradient from the litter layer to the bulk soil. Mainly in the two upper soil compartments community structure and abundance patterns of alkB were driven by the applied litter type and its degradation. Surprisingly, the differences between the compartments in one soil were more pronounced than the differences between similar compartments in the two soils studied. This indicates the necessity for analysing processes in different soil compartments to improve our mechanistic understanding of the dynamics of distinct functional groups of microbes.

To advance the understanding of the molecular mechanisms controlling microbial activities involved in carbon cycling and mitigation of environmental pollution in freshwaters, the influence of heavy metals and natural as well as xenobiotic organic compounds on laccase gene expression was quantified using quantitative real-time PCR (qRT-PCR) in an exclusively aquatic fungus (the aquatic hyphomycete Clavariopsis aquatica) for the first time. Five putative laccase genes (lcc1 to lcc5) identified in C. aquatica were differentially expressed in response to the fungal growth stage and potential laccase inducers, with certain genes being upregulated by, e.g., the lignocellulose breakdown product vanillic acid, the endocrine disruptor technical nonylphenol, manganese, and zinc. lcc4 is inducible by vanillic acid and most likely encodes an extracellular laccase already excreted during the trophophase of the organism, suggesting a function during fungal substrate colonization. Surprisingly, unlike many laccases of terrestrial fungi, none of the C. aquatica laccase genes was found to be upregulated by copper. However, copper strongly increases extracellular laccase activity in C. aquatica, possibly due to stabilization of the copper-containing catalytic center of the enzyme. Copper was found to half-saturate laccase activity already at about 1.8 μM, in favor of a fungal adaptation to low copper concentrations of aquatic habitats.

Bacterial degradation is an ecosystem service that offers a promising method for the remediation of contaminated soils. To assess the dynamics and efficiency of bacterial degradation, reliable microbial simulation models, along with the relevant processes, are required. We present an approach aimed at improving reliability by studying the relevance and implications of an important concept from theoretical ecology in the context of a bacterial system: conditional dispersal denoting that the dispersal strategy depends on environmental conditions. Different dispersal strategies, which either incorporate or neglect this concept, are implemented in a bacterial model and results are compared to data obtained from laboratory experiments with Pseudomonas putida colonies growing on glucose agar. Our results show that, with respect to the condition of resource uptake, the model's correspondence to experimental data is significantly higher for conditional than for unconditional bacterial dispersal. In particular, these results support the hypothesis that bacteria disperse less when resources are abundant. We also show that the dispersal strategy has a considerable impact on model predictions for bacterial degradation of resources: disregarding conditional bacterial dispersal can lead to overestimations when assessing the performance of this ecosystem service.

Positive biodiversity-ecosystem functioning relationships are generally attributed to two mechanisms: complementarity and selection. These mechanisms have been primarily examined using plant communities, whereas bacterial communities remain largely unexplored. Moreover, it remains uncertain how predation by single or multiple predators affects these mechanisms. Here using 465 bacterial microcosms, we show that multiple predation by protists results in positive bacterial diversity effects on bacterial yields (colony-forming units) possibly due to an increased complementarity and evenness among bacterial species. By mathematically partitioning the biodiversity effects, we demonstrate that competitive interactions in diverse communities are reduced and the growth of subdominant species is enhanced. We envisage that, including diversity gradients at other trophic levels, in biodiversity-ecosystem functioning research is a key to understanding and managing ecosystem processes. Such level of manipulation can be achieved best in microbial model systems, which are powerful tools for fundamental hypothesis-driven experiments and the investigation of general ecological theories.

While antibiotics are frequently found in the environment, their biodegradability and ecotoxicological effects are not well understood. Ciprofloxacin inhibits active and growing microorganisms and therefore can represent an important risk for the environment, especially for soil microbial ecology and microbial ecosystem services. We investigated the biodegradation of (14)C-ciprofloxacin in water and soil following OECD tests (301B, 307) to compare its fate in both systems. Ciprofloxacin is recalcitrant to biodegradation and transformation in the aqueous system. However, some mineralisation was observed in soil. The lower bioavailability of ciprofloxacin seems to reduce the compound's toxicity against microorganisms and allows its biodegradation. Moreover, ciprofloxacin strongly inhibits the microbial activities in both systems. Higher inhibition was observed in water than in soil and although its antimicrobial potency is reduced by sorption and aging in soil, ciprofloxacin remains biologically active over time. Therefore sorption does not completely eliminate the effects of this compound., (Copyright © 2011 Elsevier B.V. All rights reserved.)

Our experiments addressed systemic metabolic effects in above-ground plant tissue as part of the plant's response to the arbuscular mycorrhizal (AM) interaction. Due to the physiology of this interaction, we expected effects in the areas of plant mineral nutrition, carbon allocation and stress-related metabolism, but also a notable dependence of respective metabolic changes on environmental conditions and on plant developmental programs. To assess these issues, we analyzed metabolite profiles from mycorrhizal and non-mycorrhizal Lotus japonicus grown under greenhouse conditions at three different time points in the growing season in three different above-ground organs (flowers, sink leaves and source leaves). Statistical analysis of our data revealed a number of significant changes in individual experiments with little overlap between these experiments, indicating the expected impact of external conditions on the plant's response to AM colonization. Partial least square-discriminant analysis (PLS-DA) nevertheless revealed considerable similarities between the datasets, and loading analysis of the component separating mycorrhizal and non-mycorrhizal plants allowed the defining of a core set of metabolites responsible for this separation. This core set was observed in experiments with and without mycorrhiza-induced growth effects. It corroborated trends already indicated by the significant changes from individual experiments and suggested a negative systemic impact of AM colonization on central catabolic metabolism as well as on amino acid metabolism. In addition, metabolic signals for an increase in stress experienced by plant tissue were recorded in flowers and source leaves.

The spatio-temporal distribution of subsurface microorganisms determines their efficiency in providing essential ecosystem services such as the degradation of organic matter, the remineralization of carbon and nitrogen, or the remediation of anthropogenic contaminants. Populations of motile, chemotactic bacteria have been shown to be capable of pattern formation even in the absence of environmental heterogeneities. Focusing on the water saturated domain of the subsurface (e.g., aquatic sediments, porous aquifers), we analyze this innate capability of bacterial populations in an idealized model of a homogeneous, saturated porous medium. Considering a linear array of connected, identical microhabitats populated by motile, chemotactic bacterial cells, we identify prerequisites for pattern formation, analyze types of patterns, and assess their impact on substrate utilization. In our model, substrate supplied to the microhabitats facilitates bacterial growth, and microbial cells can migrate between neighboring microhabitats due to (i) random motility, (ii) chemotaxis towards substrate, and (iii) self-attraction. A precondition for inhomogeneous population patterns is analytically derived, stating that patterns are possible if the self-attraction exceeds a threshold defined by the random motility and the steady state population density in the microhabitats. An individual-based implementation of the model shows that static and dynamic population patterns can unfold. Degradation efficiency is highest for homogeneous bacterial distributions and decreases as pattern formation commences. If during biostimulation efforts the carrying capacity of the microhabitats is successively increased, simulation results show that degradation efficiency can unexpectedly decrease when the pattern formation threshold is crossed., (Copyright © 2011 Elsevier Ltd. All rights reserved.)

Successful biodegradation of organic soil pollutants depends on their bioavailability to catabolically active microorganisms. In particular, environmental heterogeneities often limit bacterial access to pollutants. Experimental and modelling studies revealed that fungal networks can facilitate bacterial dispersal and may thereby improve pollutant bioavailability. Here, we investigate the influence of such bacterial dispersal networks on biodegradation performance under spatially heterogeneous abiotic conditions using a process-based simulation model. To match typical situations in polluted soils, two types of abiotic conditions are studied: heterogeneous bacterial dispersal conditions and heterogeneous initial resource distributions. The model predicts that networks facilitating bacterial dispersal can enhance biodegradation performance for a wide range of these conditions. Additionally, the time horizon over which this performance is assessed and the network's spatial configuration are key factors determining the degree of biodegradation improvement. Our results support the idea of stimulating the establishment of fungal mycelia for enhanced bioremediation of polluted soils., (Copyright © 2011 Elsevier Ltd. All rights reserved.)

The pH-value played a crucial role for the development and current production of anodic microbial electroactive biofilms. It was demonstrated that only a narrow pH-window, ranging from pH 6 to 9, was suitable for growth and operation of biofilms derived from pH-neutral wastewater. Any stronger deviation from pH neutral conditions led to a substantial decrease in the biofilm performance. Thus, average current densities of 151, 821 and 730 μA cm(-2) were measured for anode biofilms grown and operated at pH 6, 7 and 9 respectively. The microbial diversity of the anode chamber community during the biofilm selection process was studied using the low cost method flow-cytometry. Thereby, it was demonstrated that the pH value as well as the microbial inocula had an impact on the resulting anode community structure. As shown by cyclic voltammetry the electron transfer thermodynamics of the biofilms was strongly depending on the solution's pH-value., (Copyright © 2011 Elsevier Ltd. All rights reserved.)

Fourier-transform infrared (FT-IR) spectroscopy is known as a high-resolution method for the rapid identification of pure cultures of microorganisms. Here, we evaluated FT-IR as a method for the quantification of bacterial populations in binary mixed cultures consisting of Pseudomonas putida and Rhodococcus ruber. A calibration procedure based on Principal Component Regression was developed for estimating the ratio of the bacterial species. Data for method calibration were gained from pure cultures and artificially assembled communities of known ratios of the two member populations. Moreover, to account for physiological variability, FT-IR measurements were performed with organisms sampled at different growth phases. Measurements and data analyses were subsequently applied to growing mixed cultures revealing that growth of R. ruber was almost completely suppressed in co-culture with P. putida. Population ratios obtained by fatty acid analysis as an independent reference method were in high agreement with the FT-IR derived ratios., (Copyright © 2011 Elsevier B.V. All rights reserved.)

Natural microbial communities generally have an unknown structure and composition because of their still not yet cultivable members. Therefore, understanding the relationships among the bacterial members, prediction of their behaviour, and controlling their functions are difficult and often only partly successful endeavours to date. This study aims to test a new idea that allows to follow community dynamics on the basis of a simple concept. Terminal restriction fragment length polymorphism (T-RFLP) analysis of bacterial 16S ribosomal RNA genes was used to describe a community profile that we define as composition of a community. Flow cytometry and analysis of DNA contents and forward scatter characteristics of the single cells were used to describe a community profile, which we define as structure of a community. Both approaches were brought together by a non-metric multidimensional scaling (n-MDS) for trend interpretation of changes in the complex community data sets. This was done on the basis of a graphical evaluation of the cytometric data, leading to the newly developed Dalmatian plot tool, which gave an unexpected insight into the dynamics of the unknown bacterial members of the investigated natural microbial community. The approach presented here was compared with other techniques described in the literature. The microbial community investigated in this study was obtained from a BTEX contaminated anoxic aquifer. The indigenous bacteria were allowed to colonise in situ microcosms consisting of activated carbon. These microcosms were amended with benzene and one of the electron acceptors nitrate, sulphate or ferric iron to stimulate microbial growth. The data obtained in this study indicated that the composition (via T-RFLP) and structure (via flow cytometry) of the natural bacterial community were influenced by the hydro-geochemical conditions in the test site, but also by the supplied electron acceptors, which led to distinct shifts in relative abundances of specific community members. It was concluded that engineered environments can be successfully monitored by single cell analytics in combination with established molecular tools and sophisticated statistical analyses, a combination that holds great promise for studying and monitoring natural microbial community behaviour.

Electrokinetically stimulated bioremediation of soils (electro-bioremediation) requires that the application of weak electric fields has no negative effect on the contaminant degrading microbial communities. This study evaluated the hypothesis that weak direct electric current (DC) fields per se do not negatively influence the physiology and composition of soil microbial communities given that secondary electrokinetic phenomena such as soil pH changes and temperatures are minimized. Mildly buffered, water-saturated laboratory mesocosms with agricultural soil were subjected for 34 days to a constant electric field (X=1.4 V cm(-1); J approximately 1.0 mA cm(-2)) and the spatiotemporal changes of soil microbial communities assessed by fingerprints of phospholipids fatty acids (PLFA) and terminal restriction fragment length polymorphisms (T-RFLP) of bacterial 16S rRNA genes. DC-induced electrolysis of the pore water led to pH changes (<1.5 pH units) in the immediate vicinity of the electrodes and concomitant distinct soil microbial community changes. By contrast, DC-treated bulk soil distant to the electrodes showed no pH changes and developed similar PLFA- and T-RFLP-fingerprints as control soil in the absence of DC. Our data suggest that the presence of an electric field, if suitably applied, will not influence the composition and physiology of soil microbial communities and hence not affect their potential to biodegrade contaminants., (Copyright 2010 Elsevier B.V. All rights reserved.)

Background: Stable isotope probing (SIP) technique was developed to link function, structure and activity of microbial cultures metabolizing carbon and nitrogen containing substrates to synthesize their biomass. Currently, available methods are restricted solely to the estimation of fully saturated heavy stable isotope incorporation and convenient methods with sufficient accuracy are still missing. However in order to track carbon fluxes in microbial communities new methods are required that allow the calculation of partial incorporation into biomolecules., Results: In this study, we use the characteristics of the so-called 'half decimal place rule' (HDPR) in order to accurately calculate the partial13C incorporation in peptides from enzymatic digested proteins. Due to the clade-crossing universality of proteins within bacteria, any available high-resolution mass spectrometry generated dataset consisting of tryptically-digested peptides can be used as reference.We used a freely available peptide mass dataset from Mycobacterium tuberculosis consisting of 315,579 entries. From this the error of estimated versus known heavy stable isotope incorporation from an increasing number of randomly drawn peptide sub-samples (100 times each; no repetition) was calculated. To acquire an estimated incorporation error of less than 5 atom %, about 100 peptide masses were needed. Finally, for testing the general applicability of our method, peptide masses of tryptically digested proteins from Pseudomonas putida ML2 grown on labeled substrate of various known concentrations were used and13C isotopic incorporation was successfully predicted. An easy-to-use script 1 was further developed to guide users through the calculation procedure for their own data series., Conclusion: Our method is valuable for estimating13C incorporation into peptides/proteins accurately and with high sensitivity. Generally, our method holds promise for wider applications in qualitative and especially quantitative proteomics.

The metabolic incorporation of stable isotopes such as (13)C or (15)N into proteins has become a powerful tool for qualitative and quantitative proteome studies. We recently introduced a method that monitors heavy isotope incorporation into proteins and presented data revealing the metabolic activity of various species in a microbial consortium using this technique. To further develop our method using an liquid chromatography (LC)-mass spectrometry (MS)-based approach, we present here a novel approach for calculating the incorporation level of (13)C into peptides by using the information given in the decimal places of peptide masses obtained by modern high-resolution MS. In the present study, the applicability of this approach is demonstrated using Pseudomonas putida ML2 proteins uniformly labeled via the consumption of [(13)C(6)]benzene present in the medium at concentrations of 0, 10, 25, 50, and 100 atom %. The incorporation of (13)C was calculated on the basis of several labeled peptides derived from one band on an SDS-PAGE gel. The accuracy of the calculated incorporation level depended upon the number of peptide masses included in the analysis, and it was observed that at least 100 peptide masses were required to reduce the deviation below 4 atom %. This accuracy was comparable with calculations of incorporation based on the isotope envelope. Furthermore, this method can be extended to the calculation of the labeling efficiency for a wide range of biomolecules, including RNA and DNA. The technique will therefore allow a highly accurate determination of the carbon flux in microbial consortia with a direct approach based solely on LC-MS.

The dynamics and composition of microbial communities in the aqueous phase of a model wetland supplied with cis- and trans-1,2-dichloroethenes (DCE)-contaminated groundwater was characterized. PCR-denaturing gradient gel electrophoresis analysis of water samples obtained from different parts of the wetland revealed that changes of the bacterial community structure coincided with a succession of the hydrochemical conditions in the wetland, from oxic towards anoxic conditions. During this transition phase, the appearance of vinyl chloride and ethene correlated with the presence of putative dechlorinating bacteria (Dehalococcoides spp., Geobacter spp. and Dehalobacter spp.). Additionally, a shift of the DCE isotopic composition indicated the progressive prevalence of reductive dechlorination in the wetland. Although the DCE degradation processes varied over time, biodegradation activity was maintained in the wetland system. 16S rRNA gene libraries revealed that Proteobacteria accounted for >50% of 16S rRNA genes clone libraries, whereas approximately 17% of the sequences from the wetland were related to sulphate reducers. Based on a multiple-method approach, this study illustrates the linkage between microbial community dynamics and composition, changes of hydrochemical conditions and processes of DCE degradation in a wetland system.

Electrical capacitance has been discussed as a real time measure for living biomass concentration in technical bioreactors such as brewery (fermentation) tanks. Commonly, a linear correlation between biomass concentration and capacitance is assumed. While following the growth and subsequent lipid formation of the yeast Arxula adeninivorans we observed non-linearity between biomass concentration and capacitance. Capacitance deviation from linearity coincided with incipient lipid formation and depended on the intracellular lipid content. As the extent of deviation between capacitance and biomass concentration was proportional to the lipid concentration, it was considered as a quantitative measure of intracellular product formation. The correlation between shifts in dielectric relaxation (summarized as characteristic frequency of the Cole-Cole equation) and lipid content could not be explained by interfacial polarization on the lipid droplets alone. However, the parameters of the Cole-Cole equation were found to be a clear indicator for different phases of growth and lipid production. Integrating all results in a redundancy analysis (RDA), we were able to accurately describe the formation of cellular lipid inclusions. Our measurements are thus potentially valuable as components of future bioprocess control strategies targeting intracellular products such as proteins or biopolyesters.

Bioremediation technologies and many environmentally sound biosyntheses rely on the catalytic potential of whole cells. For analyzing and controlling such processes robust real-time indicators for the concentration of intact cells such as impedance are required. The conventional method measures the capacitances of cell suspensions at one or two frequencies and correlates them with biomass concentrations. However, cell inclusions such as lipid droplets or overproduced enzymes may block intracellular ion paths, thereby possibly modifying the dielectric properties of the cells. To test the hypothesis that the total impedance spectrum into the analysis may provide useful information about cell inclusions, the impedance spectrum of a technical culture of the oleaginous yeast Arxula adeninivorans was measured and evaluated every 15s. This yeast is a good test object since it stores the excess of assimilated carbon in experimentally controllable lipid droplets. Upon correction for possible impedance signal interferences, we derived different empirical methods suitable to indicate incipient lipid formation. The methods were designed to act on-line and are thus principally suited for real-time monitoring of cell inclusions. In search for optimised bioprocess monitoring we tested a heuristic spectrum analysis using integrative statistics (RDA). With this approach we were able to accurately detect the formation of cell inclusions, which is potentially valuable for future bioprocess control strategies.

The diversity and dynamics of a bacterial community extracted from an exploited oil field with high natural soil salinity near Comodoro Rivadavia in Patagonia (Argentina) were investigated. Community shifts during long-term incubation with diesel fuel at four salinities between 0 and 20% NaCl were monitored by single-strand conformation polymorphism community fingerprinting of the PCR-amplified V4-V5 region of the 16S rRNA genes. Information obtained by this qualitative approach was extended by flow cytometric analysis to follow quantitatively the dynamics of community structures at different salinities. Dominant and newly developing clusters of individuals visualized via their DNA patterns versus cell sizes were used to identify the subcommunities primarily involved in the degradation process. To determine the most active species, subcommunities were separated physically by high-resolution cell sorting and subsequent phylogenetic identification by 16S rRNA gene sequencing. Reduced salinity favored the dominance of Sphingomonas spp., whereas at elevated salinities, Ralstonia spp. and a number of halophilic genera, including Halomonas, Dietzia, and Alcanivorax, were identified. The combination of cytometric sorting with molecular characterization allowed us to monitor community adaptation and to identify active and proliferating subcommunities.