Microbial nitrogen and phosphorus co-limitation across permafrost region

The status of plant and microbial nutrient limitation have profound impacts on ecosystem carbon cycle in permafrost areas, which store large amounts of carbon and experience pronounced climatic warming. Despite the long-term standing paradigm assumes that cold ecosystems primarily have nitrogen deficiency, large-scale empirical tests of microbial nutrient limitation are lacking. Here we assessed the potential microbial nutrient limitation across the Tibetan alpine permafrost region, using the combination of enzymatic and elemental stoichiometry, genes abundance and fertilization method. In contrast with the traditional view, the four independent approaches congruently detected widespread microbial nitrogen and phosphorus co-limitation in both the surface soil and deep permafrost deposits, with stronger limitation in the topsoil. Further analysis revealed that soil resources stoichiometry and microbial community composition were the two best predictors of the magnitude of microbial nutrient limitation. High ratio of available soil carbon to nutrient and low fungal/bacterial ratio corresponded to strong microbial nutrient limitation. These findings suggest that warming-induced enhancement in soil nutrient availability could stimulate microbial activity, and probably amplify soil carbon losses from permafrost areas.     

The start of frozen dates over northern permafrost regions with the changing climate

The soil freeze–thaw cycle in the permafrost regions has a significant impact on regional surface energy and water balance. Although increasing efforts have been made to understand the responses of spring thawing to climate change, the mechanisms controlling the global interannual variability of the start date of permafrost frozen (SOF) remain unclear. Using long-term SOF from the combinations of multiple satellite microwave sensors between 1979 and 2020, and analytical techniques, including partial correlation, ridge regression, path analysis, and machine learning, we explored the responses of SOF to multiple climate change factors, including warming (surface and air temperature), start date of permafrost thawing (SOT), soil properties (soil temperature and volume of water), and the snow depth water equivalent (SDWE). Overall, climate warming exhibited the maximum control on SOF, but SOT in spring was also an important driver of SOF variability; among the 65.9% significant SOT and SOF correlations, 79.3% were positive, indicating an overall earlier thawing would contribute to an earlier frozen in winter. The machine learning analysis also suggested that apart from warming, SOT ranked as the second most important determinant of SOF. Therefore, we identified the mechanism responsible for the SOT–SOF relationship using the SEM analysis, which revealed that soil temperature change exhibited the maximum effect on this relationship, irrespective of the permafrost type. Finally, we analyzed the temporal changes in these responses using the moving window approach and found increased effect of soil warming on SOF. In conclusion, these results provide important insights into understanding and predicting SOF variations with future climate change.     

Environmental and physical controls on northern terrestrial methane emissions across permafrost zones

Methane (CH₄) emissions from the northern high‐latitude region represent potentially significant biogeochemical feedbacks to the climate system. We compiled a database of growing‐season CH₄ emissions from terrestrial ecosystems located across permafrost zones, including 303 sites described in 65 studies. Data on environmental and physical variables, including permafrost conditions, were used to assess controls on CH₄ emissions. Water table position, soil temperature, and vegetation composition strongly influenced emissions and had interacting effects. Sites with a dense sedge cover had higher emissions than other sites at comparable water table positions, and this was an effect that was more pronounced at low soil temperatures. Sensitivity analysis suggested that CH₄ emissions from ecosystems where the water table on average is at or above the soil surface (wet tundra, fen underlain by permafrost, and littoral ecosystems) are more sensitive to variability in soil temperature than drier ecosystems (palsa dry tundra, bog, and fen), whereas the latter ecosystems conversely are relatively more sensitive to changes of the water table position. Sites with near‐surface permafrost had lower CH₄ fluxes than sites without permafrost at comparable water table positions, a difference that was explained by lower soil temperatures. Neither the active layer depth nor the organic soil layer depth was related to CH₄ emissions. Permafrost thaw in lowland regions is often associated with increased soil moisture, higher soil temperatures, and increased sedge cover. In our database, lowland thermokarst sites generally had higher emissions than adjacent sites with intact permafrost, but emissions from thermokarst sites were not statistically higher than emissions from permafrost‐free sites with comparable environmental conditions. Overall, these results suggest that future changes to terrestrial high‐latitude CH₄ emissions will be more proximately related to changes in moisture, soil temperature, and vegetation composition than to increased availability of organic matter following permafrost thaw.     

Microbial biogeography of drinking water: patterns in phylogenetic diversity across space and time

In this study, we collected water from different locations in 32 drinking water distribution networks in the Netherlands and analysed the spatial and temporal variation in microbial community composition by high‐throughput sequencing of 16S rRNA gene amplicons. We observed that microbial community compositions of raw source and processed water were very different for each distribution network sampled. In each network, major differences in community compositions were observed between raw and processed water, although community structures of processed water did not differ substantially from end‐point tap water. End‐point water samples within the same distribution network revealed very similar community structures. Network‐specific communities were shown to be surprisingly stable in time. Biofilm communities sampled from domestic water metres varied distinctly between households and showed no resemblance to planktonic communities within the same distribution networks. Our findings demonstrate that high‐throughput sequencing provides a powerful and sensitive tool to probe microbial community composition in drinking water distribution systems. Furthermore, this approach can be used to quantitatively compare the microbial communities to match end‐point water samples to specific distribution networks. Insight in the ecology of drinking water distribution systems will facilitate the development of effective control strategies that will ensure safe and high‐quality drinking water.     

Microbial biogeography of public restroom surfaces

We spend the majority of our lives indoors where we are constantly exposed to bacteria residing on surfaces. However, the diversity of these surface-associated communities is largely unknown. We explored the biogeographical patterns exhibited by bacteria across ten surfaces within each of twelve public restrooms. Using high-throughput barcoded pyrosequencing of the 16 S rRNA gene, we identified 19 bacterial phyla across all surfaces. Most sequences belonged to four phyla: Actinobacteria, Bacteriodetes, Firmicutes and Proteobacteria. The communities clustered into three general categories: those found on surfaces associated with toilets, those on the restroom floor, and those found on surfaces routinely touched with hands. On toilet surfaces, gut-associated taxa were more prevalent, suggesting fecal contamination of these surfaces. Floor surfaces were the most diverse of all communities and contained several taxa commonly found in soils. Skin-associated bacteria, especially the Propionibacteriaceae, dominated surfaces routinely touched with our hands. Certain taxa were more common in female than in male restrooms as vagina-associated Lactobacillaceae were widely distributed in female restrooms, likely from urine contamination. Use of the SourceTracker algorithm confirmed many of our taxonomic observations as human skin was the primary source of bacteria on restroom surfaces. Overall, these results demonstrate that restroom surfaces host relatively diverse microbial communities dominated by human-associated bacteria with clear linkages between communities on or in different body sites and those communities found on restroom surfaces. More generally, this work is relevant to the public health field as we show that human-associated microbes are commonly found on restroom surfaces suggesting that bacterial pathogens could readily be transmitted between individuals by the touching of surfaces. Furthermore, we demonstrate that we can use high-throughput analyses of bacterial communities to determine sources of bacteria on indoor surfaces, an approach which could be used to track pathogen transmission and test the efficacy of hygiene practices.     

Ecosystem carbon response of an Arctic peatland to simulated permafrost thaw

Permafrost peatlands are biogeochemical hot spots in the Arctic as they store vast amounts of carbon. Permafrost thaw could release part of these long‐term immobile carbon stocks as the greenhouse gases (GHGs) carbon dioxide (CO₂) and methane (CH₄) to the atmosphere, but how much, at which time‐span and as which gaseous carbon species is still highly uncertain. Here we assess the effect of permafrost thaw on GHG dynamics under different moisture and vegetation scenarios in a permafrost peatland. A novel experimental approach using intact plant–soil systems (mesocosms) allowed us to simulate permafrost thaw under near‐natural conditions. We monitored GHG flux dynamics via high‐resolution flow‐through gas measurements, combined with detailed monitoring of soil GHG concentration dynamics, yielding insights into GHG production and consumption potential of individual soil layers. Thawing the upper 10–15 cm of permafrost under dry conditions increased CO₂ emissions to the atmosphere (without vegetation: 0.74 ± 0.49 vs. 0.84 ± 0.60 g CO₂–C m^?2 day^?1; with vegetation: 1.20 ± 0.50 vs. 1.32 ± 0.60 g CO₂–C m^?2 day^?1, mean ± SD, pre‐ and post‐thaw, respectively). Radiocarbon dating (¹⁴C) of respired CO₂, supported by an independent curve‐fitting approach, showed a clear contribution (9%–27%) of old carbon to this enhanced post‐thaw CO₂ flux. Elevated concentrations of CO₂, CH₄, and dissolved organic carbon at depth indicated not just pulse emissions during the thawing process, but sustained decomposition and GHG production from thawed permafrost. Oxidation of CH₄ in the peat column, however, prevented CH₄ release to the atmosphere. Importantly, we show here that, under dry conditions, peatlands strengthen the permafrost–carbon feedback by adding to the atmospheric CO₂ burden post‐thaw. However, as long as the water table remains low, our results reveal a strong CH₄ sink capacity in these types of Arctic ecosystems pre‐ and post‐thaw, with the potential to compensate part of the permafrost CO₂ losses over longer timescales.     

Spatial and environmental factors contributing to phytoplankton biogeography and biodiversity in mountain ponds across a large geographic area

Aquatic Ecology - Exploring phytoplankton biodiversity and biogeographic patterns, and the factors that control them, can help to understand the structure and function of aquatic ecosystems. We...     

Integrating ecology with biogeography using landscape characteristics: a case study of subtidal habitat across continental Australia

Aim We aimed to redress a current limitation of local ecological studies (i.e. piecemeal information on specific taxa) by integrating existing ecological knowledge with quantifiable patterns in primary habitat (i.e. composition, distribution and cover) from local to continental scales. By achieving this aim, we sought to provide a biogeographical framework for the interpretation of variation in the ecology of, and threats to, subtidal rocky landscapes. Location The subtidal rocky coast of continental Australia, with longitudinal comparisons spanning > 4000 km of southern coast (115°03′ E–153°60′ E) between latitudes of 33°05′ S and 35°36′ S, and latitudinal comparisons across 26°40′ S to 37°08′ S of eastern Australia. Methods The frequency and size of patches of major benthic habitat were quantified to indicate contemporary function (ecology) and to establish patterns that may result from contrasting regional‐scale processes (biogeography). This was achieved by quantifying the composition and patchiness of key subtidal habitats across the continent and relating them to the known ecology of subsets of locations in each region. A nested design of several spatial scales (1000s, 100s, 10–1 km) was adopted to distinguish patterns at local through to biogeographical scales. Results We show biogeography (in terms of longitude and latitude) to have a fundamental influence on the patterns of abundance and composition of subtidal habitats across regional (1000s of kilometres) to local (10s of kilometres to metres) scales. Across the continent, the most fundamental patterns related to (1) the proportion of rock covered by kelp forests, as related to particular functional groups of herbivores, and (2) the small‐scale heterogeneity (metres) that characterizes these forests. Main conclusions We interpret these results within a framework of alternative processes known to maintain habitat heterogeneity across these regions (e.g. productivity versus consumption as shapers of habitat structure). These interpretations illustrate how regional differences in ecological patterns and processes can create contradictory outcomes for the management of natural resources. We suggest that researchers and managers of natural resources alike may benefit from understanding local issues (e.g. the effects of fishing and its synergies with water pollution) in their biogeographical contexts.     

Microbial biogeography: putting microorganisms on the map

We review the biogeography of microorganisms in light of the biogeography of macroorganisms. A large body of research supports the idea that free-living microbial taxa exhibit biogeographic patterns. Current evidence confirms that, as proposed by the Baas-Becking hypothesis, 'the environment selects' and is, in part, responsible for spatial variation in microbial diversity. However, recent studies also dispute the idea that 'everything is everywhere'. We also consider how the processes that generate and maintain biogeographic patterns in macroorganisms could operate in the microbial world.     

Microbial biogeography across a full-scale wastewater treatment plant transect: evidence for immigration between coupled processes

Wastewater treatment plants use a variety of bioreactor types and configurations to remove organic matter and nutrients. Little is known regarding the effects of different configurations and within-plant immigration on microbial community dynamics. Previously, we found that the structure of ammonia-oxidizing bacterial (AOB) communities in a full-scale dispersed growth activated sludge bioreactor correlated strongly with levels of NO₂ ^? entering the reactor from an upstream trickling filter. Here, to further examine this puzzling association, we profile within-plant microbial biogeography (spatial variation) and test the hypothesis that substantial microbial immigration occurs along a transect (raw influent, trickling filter biofilm, trickling filter effluent, and activated sludge) at the same full-scale wastewater treatment plant. AOB amoA gene abundance increased >30-fold between influent and trickling filter effluent concomitant with NO₂ ^? production, indicating unexpected growth and activity of AOB within the trickling filter. Nitrosomonas europaea was the dominant AOB phylotype in trickling filter biofilm and effluent, while a distinct “Nitrosomonas-like” lineage dominated in activated sludge. Prior time series indicated that this “Nitrosomonas-like” lineage was dominant when NO₂ ^? levels in the trickling filter effluent (i.e., activated sludge influent) were low, while N. europaea became dominant in the activated sludge when NO₂ ^? levels were high. This is consistent with the hypothesis that NO₂ ^? production may cooccur with biofilm sloughing, releasing N. europaea from the trickling filter into the activated sludge bioreactor. Phylogenetic microarray (PhyloChip) analyses revealed significant spatial variation in taxonomic diversity, including a large excess of methanogens in the trickling filter relative to activated sludge and attenuation of Enterobacteriaceae across the transect, and demonstrated transport of a highly diverse microbial community via the trickling filter effluent to the activated sludge bioreactor. Our results provide compelling evidence that substantial immigration between coupled process units occurs and may exert significant influence over microbial community dynamics within staged bioreactors.     

PermaBN: A Bayesian Network framework to help predict permafrost thaw in the Arctic

Rising global temperatures are a threat to the current state of the Arctic. In particular, permafrost degradation has been impacting the terrestrial cryosphere in many ways, including effects on carbon cycling and the global climate, regional hydrological connectivity and ecosystem dynamics, as well as human health and infrastructure. However, the ability to simulate permafrost dynamics under future climate projections is limited, and model outputs are often associated with large uncertainties. A model structured on a Bayesian Network is presented to address existing limitations in the representation of physically complex processes and the limited availability of observational data. A strength of Bayesian methods over more traditional modeling methods is the ability to integrate various types of evidence (i.e., observations, model outputs, expert assessments) into a single model by mapping the evidence into probability distributions. Here, we outline PermaBN, a new modeling framework, to simulate permafrost thaw in the continuous permafrost region of the Arctic. Pre-validation and expert assessment validation results show that the model produces estimations of permafrost thaw depth that are consistent with current research, i.e., thaw depth increases during the snow-free season under initial conditions favoring warming temperatures, lowered soil moisture conditions, and low active layer ice content. Using a case study from northwestern Canada to evaluate PermaBN, we show that model performance is enhanced when certainty about the system components increases for known scenarios described by observations directly integrated into the model; in this case, insulation properties from vegetation were integrated to the model. Overall, PermaBN could provide informative predictions about permafrost dynamics without high computational cost and with the ability to integrate multiple types of evidence that traditional physics-based models sometimes do not account for, allowing PermaBN to be applied to carbon modeling studies, infrastructure hazard assessments, and policy decisions aimed at mitigation of, and adaptation to, permafrost degradation.     

Threshold loss of discontinuous permafrost and landscape evolution

This study demonstrates linkages between the 1997/1998 El Niño/Southern Oscillation index and a threshold shift to increased permafrost loss within a southern Taiga Plains watershed, Northwest Territories, Canada. Three‐dimensional contraction of permafrost plateaus and changes in vegetation structural characteristics are determined from multitemporal airborne Light Detection And Ranging (LiDAR) surveys in 2008, 2011 and 2015. Morphological changes in permafrost cover are compared with optical image analogues from 1970, 1977, 2000 and 2008 and time‐series hydro‐climate data. Results demonstrate that significant changes in air temperature, precipitation, runoff and a shortening of the snow‐covered season by 35 days (1998–2014) and 50 days (1998 only) occurred after 1997. The albedo reduction associated with 35 and 50 days less snow cover leads to increases in shortwave energy receipt during the active thaw period of ~12% (3% annually) and ~16% (5% annually), respectively. From 2000 to 2015, sporadic permafrost loss accelerated from 0.19% (of total basin area) per year between 1970 and 2000 to 0.58% per year from 2000 to 2015, with a projected total loss of permafrost by ~2044. From ~1997 to 2011, we observe a corresponding shift to increased runoff ratio. However, observed increases in the proportion of snow precipitation and the volumetric contribution of permafrost loss to runoff post‐1997 (0.6–6.4% per year) cannot fully explain this shift. This suggests increases in drainage efficiency and possible losses from long‐term groundwater storage as a result of subtle terrain morphological and soil zone hydraulic conductivity changes. These hydrological changes appear coincident with high vegetation mortality at plateau margins combined with succession‐related canopy growth in some bog and fen areas, which are presumed to be drying. Similar changes in runoff response were observed at adjacent Birch, Trout and Jean Marie River watersheds indicating that observations are representative of northern Boreal sporadic permafrost/wetland watersheds in the Taiga Plains.     

Species invasions and the changing biogeography of Australian freshwater fishes

Aim By dissolving natural physical barriers to movement, human‐mediated species introductions have dramatically reshuffled the present‐day biogeography of freshwater fishes. The present study investigates whether the antiquity of Australia's freshwater ichthyofauna has been altered by the widespread invasion of non‐indigenous fish species. Location Australia. Methods Using fish presence–absence data for historical and present‐day species pools, we quantified changes in faunal similarity among major Australian drainage divisions and among river basins of north‐eastern Australia according to the Sørensen index, and related these changes to major factors of catchment disturbance that significantly alter river processes. Results Human‐mediated fish introductions have increased faunal similarity among primary drainages by an average of 3.0% (from 17.1% to 20.1% similarity). Over three‐quarters of the pairwise changes in drainage similarity were positive, indicating a strong tendency for taxonomic homogenization caused primarily by the widespread introduction of Carassius auratus, Gambusia holbrooki, Oncorhynchus mykiss and Poecilia reticulata. Faunal homogenization was highest in drainages subjected to the greatest degree of disturbance associated with human settlement, infrastructure and change in land use. Scenarios of future species invasions and extinctions indicate the continued homogenization of Australian drainages. In contrast, highly idiosyncratic introductions of species in river basins of north‐eastern Australia have decreased fish faunal similarity by an average of 1.4%. Main conclusions We found that invasive species have significantly changed the present‐day biogeography of fish by homogenizing Australian drainages and differentiating north‐eastern river basins. Decreased faunal similarity at smaller spatial scales is a result of high historical similarity in this region and reflects the dynamic nature of the homogenization process whereby sporadic introductions of new species initially decrease faunal similarity across basins. Our study points to the importance of understanding the role of invasive species in defining patterns of present‐day biogeography and preserving the antiquity of Australia's freshwater biodiversity.     

Reconstructing the evolutionary history of an endangered subspecies across the changing landscape of the Great Central Valley of California

Identifying historic patterns of population genetic diversity and connectivity is a primary challenge in efforts to re‐establish the processes that have generated and maintained genetic variation across natural landscapes. The challenge of reconstructing pattern and process is even greater in highly altered landscapes where population extinctions and dramatic demographic fluctuations in remnant populations may have substantially altered, if not eliminated, historic patterns. Here, we seek to reconstruct historic patterns of diversity and connectivity in an endangered subspecies of woodrat that now occupies only 1–2 remnant locations within the highly altered landscape of the Great Central Valley of California. We examine patterns of diversity and connectivity using 14 microsatellite loci and sequence data from a mitochondrial locus and a nuclear intron. We reconstruct temporal change in habitat availability to establish several historical scenarios that could have led to contemporary patterns of diversity, and use an approximate Bayesian computation approach to test which of these scenarios is most consistent with our observed data. We find that the Central Valley populations harbour unique genetic variation coupled with a history of admixture between two well‐differentiated species of woodrats that are currently restricted to the woodlands flanking the Valley. Our simulations also show that certain commonly used analytical approaches may fail to recover a history of admixture when populations experience severe bottlenecks subsequent to hybridization. Overall our study shows the strength of combining empirical and simulation analyses to recover the history of populations occupying highly altered landscapes.     

Seasonality of phytoplankton in northern tundra ponds

Thermokarst ponds are the most abundant type of water body in the arctic tundra, with millions occurring in the coastal plains of Alaska, Northwest Territories and Siberia. Because ice covers of at least 2 m in thickness are formed at these latitudes, tundra ponds freeze solid every winter As a result, the growing season is shortened to a range of 60 to 100 days, during which time the photoperiod is altered to a prolonged light phase. Tundra ponds are generally close to neutral in pH and low in ions, contain dissolved gases near saturation and are nutrient poor. In low arctic ponds there are two phytoplankton biomass and primary production peaks, whereas they may be only one in the high arctic. Nanoplanktonic flagellates of the Chrysophyceae and Cryptophyceae dominate the maxima. The mid-summer decline in phytoplankton in the low arctic can be attributed to a combination of phosphorus limitation and heavy grazing pressure. The cryptomonad Rhodomonas minuta Skuja is one of the most widespread phytoplankters in tundra ponds. Because of the altered photoperiods, many species do not form resting spores prior to ice formation but survive freezing in the vegetative state.     

Water circulation in the moraine ponds of northern Poland

The landscape of northern Poland is characterised by a very large number of ponds. Traditionally it has been assumed that their hydrology is determined by precipitation and evaporation, and that they are isolated from the adjacent river network. Recent studies, however, have shown that ponds contribute to river runoff for at least part of the year. Their existence is therefore additionally based on fluvial and underground water sources. In order to establish the principles of water circulation in typical ponds, we selected 14 ponds with seasonally intermittent streams. We measured water levels in these ponds and flows in the river segments that connect them. We also determined subsurface exchange fluxes from the water balance equation. Our results demonstrated that the hydrological functions of the ponds varied throughout the year and depended on the level of water storage in the pond’s catchment. When the level of retention in the pond’s catchment is low, the pond becomes a water body without surface outflow and a drainage base for groundwater. As the level of retention in the catchment rises, ponds develop surface outflows and reconnect with the river network. At this point, their main function becomes retention of water originating from subsurface and surface inflows. Any surplus water may be fed to underground or surface waters.     

Microbial diversity of Late Pleistocene Siberian permafrost samples

A metagenomic study of the Kolyma lowland permafrost samples, 20–35 thousand years, performed using a Geneclean for Ancient DNA kit (Bio101, United States), revealed 8 phylotypes which belonged to the phyla Actinobacteria and Proteobacteria. Analysis of the 16S rRNA gene clone library showed that most of the clones (48% and 29%) were represented by the genera Arthrobacter and Bradyrhizobium, respectively. For the first time microorganisms of the genera Williamsia, Bradyrhizobium, Filomicrobium and Hansschlegelia were observed in the ancient microbial communities of these ecosystems. Analysis of the isolates 16S rRNA genes revealed the presence of the microorganisms—the representatives of the phyla Firmicutes and Actinobacteria phylogenetically related to known species and being obvious representatives of novel taxa. In situ electron-microscope analysis of total preparations of the studied samples showed the presence of intact bacterial cells of different morphotypes.     

Nitrogen availability increases in a tundra ecosystem during five years of experimental permafrost thaw

Perennially frozen soil in high latitude ecosystems (permafrost) currently stores 1330–1580 Pg of carbon (C). As these ecosystems warm, the thaw and decomposition of permafrost is expected to release large amounts of C to the atmosphere. Fortunately, losses from the permafrost C pool will be partially offset by increased plant productivity. The degree to which plants are able to sequester C, however, will be determined by changing nitrogen (N) availability in these thawing soil profiles. N availability currently limits plant productivity in tundra ecosystems but plant access to N is expected improve as decomposition increases in speed and extends to deeper soil horizons. To evaluate the relationship between permafrost thaw and N availability, we monitored N cycling during 5 years of experimentally induced permafrost thaw at the Carbon in Permafrost Experimental Heating Research (CiPEHR) project. Inorganic N availability increased significantly in response to deeper thaw and greater soil moisture induced by Soil warming. This treatment also prompted a 23% increase in aboveground biomass and a 49% increase in foliar N pools. The sedge Eriophorum vaginatum responded most strongly to warming: this species explained 91% of the change in aboveground biomass during the 5 year period. Air warming had little impact when applied alone, but when applied in combination with Soil warming, growing season soil inorganic N availability was significantly reduced. These results demonstrate that there is a strong positive relationship between the depth of permafrost thaw and N availability in tundra ecosystems but that this relationship can be diminished by interactions between increased thaw, warmer air temperatures, and higher levels of soil moisture. Within 5 years of permafrost thaw, plants actively incorporate newly available N into biomass but C storage in live vascular plant biomass is unlikely to be greater than losses from deep soil C pools.