Impacts of tropospheric ozone exposure on peatland microbial consumers

Tropospheric ozone pollution is recognised as an important threat to terrestrial ecosystems but impacts on peatlands are little understood despite the importance of peat as a global carbon store. Here we investigate the impacts of three levels of elevated exposure to tropospheric ozone on peatland microbial communities with a particular focus on testate amoebae, the dominant microbial consumers. We found that in the intermediate (ambient + 25 ppb O3) and high treatments (ambient +35 ppb summer, +10 ppb year round) there were significant changes in testate amoeba communities, typified by an increase in abundance of Phyrganella spp. and loss of diversity. Phyrganella is often suggested to feed on fungi so the community change identified in our experiment might suggest that the testate amoeba response is at least partially mediated by interactions with other microbial groups. We do not find evidence for changes in numbers of undifferentiated microalgae, nematodes or rotifers but do find weak evidence for an increase in flagellates and ciliates. Our results provide the first direct data to show the impact of ozone on microbial consumers in peatlands

Ammonia exposure promotes algal biomass in an ombrotrophic peatland

Nitrogen pollution affects many peatlands with consequences for their biodiversity and ecosystem function. Microorganisms control nutrient cycling and constitute most of the biodiversity of peatlands but their response to nitrogen is poorly characterised and likely to depend on the form of deposition. Using a unique field experiment we show that ammonia exposure at realistic point source levels is associated with a general shift from heterotrophic (bacteria and fungi) to autotrophic (algal) dominance and an increase in total biomass. The biomass of larger testate amoebae increased, suggesting increased food supply for microbial predators. Results show the widespread impacts of N pollution and suggest the potential for microbial community-based bioindicators in these ecosystems

Assessing the responses of Sphagnum micro-eukaryotes to climate changes using high throughput sequencing

Current projections suggest that climate warming will be accompanied by more frequent and severe drought events. Peatlands store ca. one third of the world’s soil organic carbon. Warming and drought may cause peatlands to become carbon sources through stimulation of microbial activity increasing ecosystem respiration, with positive feedback effect on global warming. Micro-eukaryotes play a key role in the carbon cycle through food web interactions and therefore, alterations in their community structure and diversity may affect ecosystem functioning and could reflect these changes. We assessed the diversity and community composition of Sphagnum-associated eukaryotic microorganisms inhabiting peatlands and their response to experimental drought and warming using high throughput sequencing of environmental DNA. Under drier conditions, micro-eukaryotic diversity decreased, the relative abundance of autotrophs increased and that of osmotrophs (including Fungi and Peronosporomycetes) decreased. Furthermore, we identified climate change indicators that could be used as early indicators of change in peatland microbial communities and ecosystem functioning. The changes we observed indicate a shift towards a more “terrestrial” community in response to drought, in line with observed changes in the functioning of the ecosystem

Hydrological dynamics and fire history of the last 1300years in western Siberia reconstructed from a high-resolution, ombrotrophic peat archive

International audienceSiberian peatlands provide records of past changes in the continental climate of Eurasia. We analyzed a core from Mukhrino mire in western Siberia to reconstruct environmental change in this region over the last 1300 years. The pollen analysis revealed little variation of local pine-birch forests. A testate amoebae transfer function was used to generate a quantitative water-table reconstruction; pollen, plant macrofossils, and charcoal were analyzed to reconstruct changes in vegetation and fire activity. The study revealed that Mukhrino mire was wet until the Little Ice Age (LIA), when drought was recorded. Dry conditions during the LIA are consistent with other studies from central and eastern Europe, and with the pattern of carbon accumulation across the Northern Hemisphere. A significant increase in fire activity between ca. AD 1975 and 1990 may be associated with the development of the nearby city of Khanty-Mansiysk, as well as with the prevailing positive Arctic Oscillation

Significance testing testate amoeba water table reconstructions

Transfer functions are valuable tools in palaeoecology, but their output may not always be meaningful. A recently-developed statistical test ('randomTF') offers the potential to distinguish among reconstructions which are more likely to be useful, and those less so. We applied this test to a large number of reconstructions of peatland water table depth based on testate amoebae. Contrary to our expectations, a substantial majority (25 of 30) of these reconstructions gave non-significant results (P > 0.05). The underlying reasons for this outcome are unclear. We found no significant correlation between randomTF P-value and transfer function performance, the properties of the training set and reconstruction, or measures of transfer function fit. These results give cause for concern but we believe it would be extremely premature to discount the results of non-significant reconstructions. We stress the need for more critical assessment of transfer function output, replication of results and ecologically-informed interpretation of palaeoecological data

Soil protistology rebooted: 30 fundamental questions to start with

Protists are the most diverse eukaryotes. These microbes are keystone organisms of soil ecosystems and regulate essential processes of soil fertility such as nutrient cycling and plant growth. Despite this, protists have received little scientific attention, especially compared to bacteria, fungi and nematodes in soil studies. Recent methodological advances, particularly in molecular biology techniques, have made the study of soil protists more accessible, and have created a resurgence of interest in soil protistology. This ongoing revolution now enables comprehensive investigations of the structure and functioning of soil protist communities, paving the way to a new era in soil biology. Instead of providing an exhaustive review, we provide a synthesis of research gaps that should be prioritized in future studies of soil protistology to guide this rapidly developing research area. Based on a synthesis of expert opinion we propose 30 key questions covering a broad range of topics including evolution, phylogenetics, functional ecology, macroecology, paleoecology, and methodologies. These questions highlight a diversity of topics that will establish soil protistology as a hub discipline connecting different fundamental and applied fields such as ecology, biogeography, evolution, plant-microbe interactions, agronomy, and conservation biology. We are convinced that soil protistology has the potential to be one of the most exciting frontiers in biology

Uncovering microbial food webs using machine learning

Microbial trophic interactions are an important aspect of microbiomes in any ecosystem. They can reveal how microbial diversity modulates ecosystem functioning. However, uncovering microbial feeding interactions is a challenge because direct observation of predation is difficult with classical approaches such as behaviour and gut contents analyses. To overcome this issue, recent developments in trait-matching and machine-learning ap- proaches are promising for successfully inferring microbial feeding links. Here, we tested the ability of six machine-learning algorithms for predicting microbial feeding links, based on species traits and taxonomy. By incorporating organism speed, size and abundance into the model predictions, we further estimated the prob- ability of feeding links occurring. We found that the model trained with the boosted regression trees algorithm predicted feeding links between microbes best. Sensitivity analyses showed that feeding link predictions were robust against faulty predictors in the training set, and capable of predicting feeding links for empirical datasets containing up to 50% of new taxa. We cross-validated the feeding link predictions using an empirical dataset from a Sphagnum-dominated peatland with direct feeding observations for two dominant testate amoeba pred- ators. The feeding habits of the two testate amoeba species were comparable between microscopic observations and model predictions. Machine learning thus offers a means to develop robust models for studying microbial food webs. It offers a route to combine traditional observations with DNA-based sampling strategies to upscale soil biodiversity research along ecological gradients

A meta-analysis of peatland microbial diversity and function responses to climate change

International audienceClimate change threatens the capacity of peatlands to continue storing carbon (C) belowground. Microorganisms are crucial in regulating the peatland C sink function, but how climate change affects the richness, biomass and functions of peatland microbiomes still remains uncertain. Here, we conducted a global meta-analysis of the response of peatland bacterial, fungal and micro-eukaryote communities to climate change by synthesizing data from 120 climate change experiments. We show that climate drivers such as warming, drought and warming-induced vegetation shift strongly affect microbial diversity, community composition, trophic structure and functions. Using meta-analytic structural equation modelling, we developed a causal understanding among the different strands of microbial properties. We found that climate drivers influenced microbial metabolic rates, such as CO2 fixation and respiration, methane production and oxidation, directly through physiological effects, and indirectly, through microbial species turnover and shifts in the trophic structure of microbial communities. In particular, we found that the response of microbial CO2 fixation increased for each degree in air temperature gained, while the response of microbial CO2 respiration tended to decline. When extrapolated at the global peatland scale using the CMIP6 model under the SSP5-8.5 scenario, our findings suggest that the increasingly positive response of microbial CO2 fixation to temperature anomalies in northern latitudes might compensate to some extent for the possible loss of C from microbial CO2 respiration, possibly allowing peatlands to remain C sinks on long-term. Our findings have crucial implications for advancing our understanding of carbon-climate feedback from peatlands in a warming world

Testate amoebae taxonomy and trait diversity are coupled along an openness and wetness gradient in pine-dominated Baltic bogs

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Biofilm community composition is changing in remote mountain lakes with a relative increase in potentially toxigenic algae

International audienceMountain lakes provide clear drinking water to humankind but are strongly impacted by global change. Benthic biofilms are crucial for maintaining water quality in these oligotrophic lakes, yet little is known about the effects of global change on mountain biofilm communities. By combining analyses of metabarcoding data on 16S and 18S rRNA genes with climatic and environmental data, we investigated global change effects on the composition of biofilm prokaryotic and micro-eukaryotic assemblages in a five-year monitoring program of 26 Pyrenean lakes (2016–2020). Using time-decay relationships and within-lake dissimilarity modelling, we show that the composition of both prokaryotic and micro-eukaryotic biofilm communities significantly shifted and their biodiversity declined from 2016 to 2020. In particular, analyses of temporal trends with linear mixed models indicated an increase in the richness and relative abundance of cyanobacteria, including potentially toxigenic cyanobacteria, and a concomitant decrease in diatom richness and relative abundance. While these compositional shifts may be due to several drivers of global change acting simultaneously on mountain lake biota, water pH and hardness were, from our data, the main environmental variables associated with changes for both prokaryotic and micro-eukaryotic assemblages. Water pH and hardness increased in our lakes over the study period, and are known to increase in Pyrenean lakes due to the intensification of rock weathering as a result of climate change. Given predicted climate trends and if water pH and hardness do cause some changes in benthic biofilms, those changes might be further exacerbated in the future. Such biofilm compositional shifts may induce cascading effects in mountain food webs, threatening the resilience of the entire lake ecosystem. The rise in potentially toxigenic cyanobacteria also increases intoxication risks for humans, pets, wild animals, and livestock that use mountain lakes. Therefore, our study has implications for water quality, ecosystem health, public health, as well as local economies (pastoralism, tourism), and highlights the possible impacts of global change on mountain lakes