Biology subjects

Peura, S.

Publications and source records attributed to Peura, S..

13 recordsLinked to original sources

bioRxiv2022

Network analysis uncovers associations in the turnover of C1 molecules in a winter lake

The generation and consumption of single carbon molecules (CO2 and CH4) by aquatic microbial communities is an essential aspect of the global carbon budget. Organic carbon flow (warm sunlit regimes) is depicted as beginning at the surface with autochthonous fixation followed by biomass settling to sediments, CO2 respiration to the atmosphere, and outflow. We sought to broaden understanding of C1 cycling and consortia by examining the microbial community of a below-ice lake water column in which both input and output are likely disrupted due to ice cover. By analysing the microbial community composition and co-occurrence network of an ice-covered lake timeseries, we were able to identify potential consortia involved in C1 cycling. The network confirmed known associations supporting the efficacy of such analyses but also pointed to previously unknown potential associations. Further and contrary to typical organic carbon flow under warm sunlit regimes, we found support for upward flow of recently fixed carbon in cold low-light conditions under-ice in winter.

microbiology↗

bioRxiv2022

A metagenomic view on fungal diversity in freshwater lakes

Fungi are essential components in a wide range of ecosystems and while major efforts have been spent on disentangling the diversity and functional roles of fungi in terrestrial environments, our knowledge about aquatic fungi is lagging. To address this knowledge gap, we explored metagenomes from 25 lakes from the arctic and boreal zone and one tropical reservoir with the aim of describing the community structure of fungi and fungi-like organisms (Oomycota). A second objective was to identify possible environmental factors influencing the composition of the fungal communities. Our results show that the main fungal phyla and orders are the same across all the lakes despite the differences in geographic location and prevailing climate. Still, there was differential distribution of more highly resolved taxa across the lakes that accordingly featured distinct communities, possibly caused by differential availability of carbon substrates in the lakes. A more detailed classification of sequences related to the pathogenic Oomycota genus Phytophthora clearly demonstrated that while technologies now exist for sequencing entire microbial communities in great detail, we are still severely limited by insufficient coverage of eukaryotic sequences and genomes in public databases.

ecology↗

bioRxiv2022

Biogenic methane cycling is controlled by microbial cohorts

The generation and consumption of methane by aquatic microbial communities is an important contribution to the global carbon budget. We sought to broaden understanding of consortia members and interactions by combining multiple methods including analysis of natural and cultivated microbial communities. By analysing the microbial community composition and co-occurrence patterns of a lake time-series we were able to identify potential consortia involved in methane cycling. In combination with methane flux, we also analysed the community composition and co-occurrence patterns of reduced microbial model communities with inoculum from the same lake. While the network analyses confirmed many known associations, when combined with results from mixed cultures, we noted new players in methane cycling. Cultivated model communities were shown to be an effective method to explore the rarer but still important players in methane cycling and for identifying new putative members. Here we show that using multiple methods to approach the complex problem of methane cycling consortia yields not just insights into the known taxa but highlights potential new members creating new hypotheses to be tested.

microbiology↗

bioRxiv2021

Global patterns and rates of habitat transitions across the eukaryotic tree of life

The successful colonisation of new habitats has played a fundamental role during the evolution of life. Salinity is one of the strongest barriers for organisms to cross, which has resulted in the evolution of distinct marine and terrestrial (including both freshwater and soil) communities. Although microbes represent by far the vast majority of eukaryote diversity, the role of the salt barrier in shaping the diversity across the eukaryotic tree is poorly known. Traditional views suggest rare and ancient marine-terrestrial transitions, but this view is being challenged by the discovery of several recently transitioned lineages. Here, we investigate habitat evolution across the tree of eukaryotes using a unique set of taxon-rich environmental phylogenies inferred from a combination of long-read and short-read metabarcoding data spanning the ribosomal DNA operon. Our results show that overall marine and terrestrial microbial communities are phylogenetically distinct, but transitions have occurred in both directions in almost all major eukaryotic lineages, with at least 350 transition events detected. Some groups have experienced relatively high rates of transitions, most notably fungi for which crossing the salt barrier has most likely been an important aspect of their successful diversification. At the deepest phylogenetic levels, ancestral habitat reconstruction analyses suggest that eukaryotes may have first evolved in non-saline habitats, and that the two largest known eukaryotic assemblages (TSAR and Amorphea) arose in different habitats. Overall, our findings indicate that crossing the salt barrier has played an important role in eukaryotic evolution by providing new ecological niches to fill.

evolutionary biology↗

bioRxiv2021

16S rRNA gene sequences of Candidatus Methylumidiphilus (Methylococcales), a putative methanotrophic genus in lakes and ponds

A putative novel methanotrophic genus, Candidatus Methylumidiphilus (Methylococcales), was recently shown to be ubiquitous and one of the most abundant methanotrophic genera in water columns of oxygen-stratified lakes and ponds of boreal and subarctic area. However, it has probably escaped detection in many previous studies using 16S rRNA gene amplicon sequencing due to insufficient database coverage, which is because Ca. Methylumidiphilus lacks cultured representatives and previously analysed metagenome assembled genomes (MAGs) affiliated with it do not contain 16S rRNA genes. Therefore, we screened MAGs affiliated with the genus for their 16S rRNA gene sequences in a recently published lake and pond MAG dataset. Among 66 MAGs classified as Ca. Methylumidiphilus (with completeness over 40% and contamination less than 5%) originating from lakes in Finland, Sweden and Switzerland as well as from ponds in Canada, we could find 5 MAGs each containing one 1532 bp long sequence spanning the V1-V9 regions of the 16S rRNA gene. After removal of sequence redundancy, this resulted in two unique 16S rRNA gene sequences. These sequences represented two different putative species, i.e. Ca. Methylumidiphilus alinenensis (Genbank accession: OK236221) as well as another so far unnamed species of Ca. Methylumidiphilus (Genbank accession: OK236220). We suggest that including these two sequences in reference databases will enhance 16S rRNA gene - based detection of members of this genus from environmental samples.

ecology↗

bioRxiv2021

Fungal community composition along a gradient of permafrost thaw

Thermokarst activity at permafrost sites releases considerable amount of ancient carbon to the atmosphere. A large part of this carbon is released via thermokarst ponds, and fungi could be an important organismal group enabling its recycling. However, our knowledge about aquatic fungi growing in thermokarstic systems is extremely limited. In this study, we collected samples from five permafrost sites distributed across circumpolar Arctic and representing a gradient of permafrost integrity. Samples were taken from the ponds surface water, the detritus and the sediment at the bottom of the ponds. These samples were extracted for total DNA, which was then amplified using primers targeting the fungal ITS2 region of the ribosomal genes. These amplicons were sequenced using PacBio technology. Surface water samples were also collected to analyze the chemical conditions in the ponds, including nutrient status and the quality and quantity of dissolved organic carbon. This dataset gives a unique overview of the impact of the thawing permafrost on fungal communities and their potential role on carbon recycling.

ecology↗

bioRxiv2021

Comprehensive analysis of chemical and biological problems associated with browning agents used in aquatic studies

Inland waters receive and process large amounts of colored organic matter from the terrestrial surroundings. These inputs dramatically affect the chemical, physical, and biological properties of water bodies, as well as their roles as global carbon sinks and sources. To understand the complex changes associated with allochthonous inputs, experiments are needed. However, manipulative studies, especially at ecosystem scales, require large amounts of dissolved organic matter with optical and chemical properties resembling indigenous organic matter. Here we compared the chemical and biological impacts of two leonardite products (HuminFeed (HF) and SuperHume (SH)) and a freshly derived reverse osmosis concentrate of organic matter (RO) in a set of comprehensive mesocosm- and laboratory-scale experiments and analyses. The chemical properties of RO concentrate and the leonardite products were very different with leonardite products being low and RO being high in carboxylic functional groups. Light had a strong impact on the properties of leonardite products, including loss of color and increased particle formation. Furthermore, HF had drastic impacts on bacteria as light stimulated bacterial production and modified community composition, while dark conditions appeared to inhibit bacterial processes. While none of the browning agents inhibited the growth of the tested phytoplankton, Gonyostomum semen, leonardite products had detrimental effects on zooplankton abundance and Daphnia reproduction. We conclude that the effects of browning agents extracted from leonardite are in sharp contrast to those originating from terrestrially-derived DOM. Hence, they should be used with great caution in experimental studies on the consequences of terrestrial carbon for aquatic systems.

ecology↗

bioRxiv2021

Nitrate enhances anaerobic oxidation of methane in boreal lake sediments

The identity of electron acceptors in promoting anaerobic oxidation of methane (AOM) in the sediments of boreal lakes is currently unknown. Here, we studied the AOM rate of sediment slurries collected from three profundal stations of a nitrate-rich, oligo-mesotrophic, boreal lake (Lake Paajarvi, Finland), under varying nitrate concentrations using 13C-labelling. Furthermore, vertical profiles of the sediment and porewater geochemistry, and the microbial communities (16S rRNA gene and shotgun metagenomic sequencing) were analyzed. Despite geochemical data indicating that simultaneous consumption of nitrate and methane took place at the sediment layers chosen for incubations, AOM rate was not enhanced by nitrate amendments at either of the stations. AOM rate was much higher at the shallow Station 1 (0.9-6.8 nmol C cm-3 d-1) with high contents of labile phytoplankton-derived organic matter, than at the deeper stations, Station 2 (0-0.3 nmol C cm-3 d-1) and 3 (0-0.2 nmol C cm-3 d-1). Accordingly, a higher relative abundance of methanotrophic archaea (Candidatus Methanoperedens) and bacteria (Methylococcales) were observed in the layers chosen for incubations at Station 1 than at the other stations. Besides nitrate, the geochemical profiles indicated that AOM was potentially coupled with iron or sulfate reduction at all stations. Furthermore, putative nitrite-reducing methanotrophs (Ca. Methylomirabilis) were the most abundant methanotrophs above the incubation layer at Station 2 and 3, which suggests that nitrite reduction also plays a role in driving AOM in the study lake. We conclude that AOM is not uniquely coupled to nitrate reduction in sediments of nitrate-rich, oligo-mesotrophic, boreal lakes.

ecology↗

bioRxiv2020

Comprehensive dataset of shotgun metagenomes from stratified freshwater lakes and ponds

Stratified lakes and ponds featuring steep oxygen gradients are significant net sources of greenhouse gases and hotspots in the carbon cycle. Despite their significant biogeochemical roles, the microbial communities, especially in the oxygen depleted compartments, are poorly known. Here, we present a comprehensive dataset including 267 shotgun metagenomes from 41 stratified lakes and ponds mainly located in the boreal and subarctic regions, but also including one tropical reservoir and one temperate lake. For most lakes and ponds, the data includes a vertical sample set spanning from the oxic surface to the anoxic bottom layer. The majority of the samples were collected during the open water period, but also a total of 29 samples were collected from under the ice. In addition to the metagenomic sequences, the dataset includes environmental variables for the samples, such as oxygen, nutrient and organic carbon concentrations. The dataset is ideal for further exploring the microbial taxonomic and functional diversity in freshwater environments and potential climate change impacts on the functioning of these ecosystems.

ecology↗

bioRxiv2020

Freshwater Chlorobia exhibit metabolic specialization among cosmopolitan and endemic populations

Photosynthetic bacteria from the class Chlorobia (formerly phylum Chlorobi) sustain carbon fixation in anoxic water columns. They harvest light at extremely low intensities and use various inorganic electron donors to fix carbon dioxide into biomass. Until now, most information on their functional ecology and local adaptations came from isolates and merely 26 sequenced genomes that are poor representatives of natural populations. To address these limitations, we analyzed global metagenomes to profile planktonic Chlorobia cells from the oxyclines of 42 freshwater bodies, spanning subarctic to tropical regions and encompassing all four seasons. We assembled and compiled over 500 genomes, including metagenome-assembled genomes (MAGs), single-cell genomes (SAGs), and reference genomes from cultures, clustering them into 71 metagenomic operational taxonomic units (mOTUs) or "species". Of the 71 mOTUs, 57 were classified as genus Chlorobium and these mOTUs varied in relative abundance up to ~60% of the microbial communities in the sampled anoxic waters. Several Chlorobium-associated mOTUs were globally distributed whereas others were endemic to individual lakes. Although most clades encoded the ability to oxidize hydrogen, many were lacking genes for the oxidation of specific sulfur and iron substrates. Surprisingly, one globally distributed Scandinavian Chlorobium clade encoded the ability to oxidize hydrogen, sulfur, and iron, suggesting that metabolic versatility facilitated such widespread colonization. Overall, these findings provide new insights into the biogeography of the Chlorobia and the metabolic traits that facilitate niche specialization within lake ecosystems. ImportanceThe reconstruction of genomes from metagenomes has enabled unprecedented insights into the ecology and evolution of environmental microbiomes. We applied this powerful approach to 274 metagenomes collected from diverse freshwater habitats that spanned oxic and anoxic zones, sampling seasons, and latitudes. We demonstrate widespread and abundant distributions of planktonic Chlorobia-associated bacteria in hypolimnetic waters of stratified freshwater ecosystems and pinpoint nutrients that likely fuel their electron chains. Being photoautotrophs, these Chlorobia organisms also have the potential to serve as carbon sources that support metalimnetic and hypolimnetic food webs.

ecology↗

bioRxiv2018

Decreased snow cover stimulates under ice primary producers, but impairs methanotrophic capacity

Climate change scenarios anticipate decrease of spring snow cover in boreal and subarctic regions. Forest lakes are abundant in these regions and substantial contributors of methane emissions. We performed an experiment on an anoxic frozen lake and observed that the removal of snow increased light penetration through the ice into the water modifying the microbial composition across depths. A shift in photosynthetic primary production was reflected by the increase of chlorophyll a and b concentrations in the upper depths of the water column, while Chlorobia, one of the key photosynthetic bacteria in anoxic lakes, shifted to lower depths. Moreover, a decrease in abundance of methanotrophs, such as Methylococcaceae, was noted concurrently to an increase in methane concentration in the water column. These results indicate that decrease of snow cover impacts both primary production and methane production/consumption, ultimately leading to increased methane emissions after spring ice off.

ecology↗

bioRxiv2018

Novel autotrophic organisms contribute significantly to the internal carbon cycling potential of a boreal lake

The authors declare no conflict of interest\n\nFunding sources: the Academy of Finland, Science for Life Laboratories, Tryggers Foundation, the Swedish Research Council VR and the Swedish Foundation for strategic research\n\nAbstractOxygen stratified lakes are typical for the boreal zone, and also a major source of greenhouse gas emissions in the region. Due to shallow light penetration, restricting the growth of phototrophic organisms, and large allochthonous organic carbon inputs from the catchment area, the lake metabolism is expected to be dominated by heterotrophic organisms. In this study we test this assumption and show that the potential for autotrophic carbon fixation and internal carbon cycling is high throughout the water column. Further, we show that during the summer stratification carbon fixation can exceed respiration in a boreal lake even below the euphotic zone. Metagenome assembled genomes and 16S profiling of a vertical transect of the lake revealed multiple organisms in oxygen depleted compartment belonging to novel or poorly characterized phyla. Many of these organisms were chemolithotrophic, deriving their energy from reactions related to sulfur, iron and nitrogen transformations. The community as well as the functions were stratified following the redox potentials. The autotrophic potential in the lake metagenome below the oxygenic zone was high, pointing towards a need for revising our concepts of internal carbon cycling in boreal lakes. Further, the importance of chemolithoautotrophy for the internal carbon cycling suggests that many predicted climate change associated changes in the physical properties of the lake, such as altered mixing patterns, likely have consequences for the whole lake metabolism even beyond the impact to the phototrophic community.\n\nImportanceAutotrophic organisms at the base of the food web are the only life form capable of turning inorganic carbon into organic form, facilitating the survival of all other organisms. In certain environments the autotrophic production is limited by environmental conditions and the food web is supported by carbon coming from outside the ecosystem. One such environment is stratified boreal lakes, which are one of the biggest sources of greenhouse gas emissions in the boreal region. Thus, carbon cycling in these habitats is of outmost importance for the future climate. Here we demonstrate a high potential for internal carbon cycling via phototrophic and novel chemolithotrophic organisms in the dark and anoxic layers of a boreal lake. Our results significantly increase our knowledge on the microbial communities and their metabolic potential in oxygen depleted freshwaters and help to understand and predict how climate change induced alterations could impact the lake carbon dynamics.

ecology↗

bioRxiv2017

Novel Chemolithotrophic And Anoxygenic Phototrophic Genomes Extracted From Ice-Covered Boreal Lakes

Although an important fraction of the worlds lakes remains ice-covered during a large proportion of the year, little is known about the microorganisms that govern the biogeochemical processes occurring under-ice along the stratigraphic redox gradients. Reconstructed genomes provide evidence for anoxygenic photosynthesis involving fixation of carbon using reduced sulphur and iron as an electron donor in the anoxic zone of the sampled lake systems. In addition to anoxygenic photosynthesis, our molecular data reveals novel chemolithoautotrophic organisms and supports the existence of methanotrophs in bottom anoxic waters. Reconstructed genomes matched methanotrophs related to Methylobacter tundripaludum, phototrophic Chloroflexi and Chlorobia, as well as lithoautotrophic genomes affiliated to the Betaproteobacteria class and Planctomycetes phylum. Based on our in-depth characterization, complex metabolic interactomes emerge unique to each lakes redox tower and with sulfur, iron and carbon cycling tightly intertwined through chemolithotrophy and anoxygenic photosynthesis.

ecology↗