Climate warming has direct and indirect effects on microbes associated with carbon cycling in northern lakes

Northern lakes disproportionately influence the global carbon cycle, and may do so more in the future depending on how their microbial communities respond to climate warming. Microbial communities can change because of the direct effects of climate warming on their metabolism and the indirect effects of climate warming on groundwater connectivity from thawing of surrounding permafrost, especially at lower landscape positions. Here we used shotgun metagenomics to compare the taxonomic and functional gene composition of sediment microbes in 19 peatland lakes across a 1600-km permafrost transect in boreal western Canada. We found microbes responded differently to the loss of regional permafrost cover than to increases in local groundwater connectivity. These results suggest that both the direct and indirect effects of climate warming, which were respectively associated with loss of permafrost and subsequent changes in groundwater connectivity interact to change microbial composition and function. Archaeal methanogens and genes involved in all major methanogenesis pathways were more abundant in warmer regions with less permafrost, but higher groundwater connectivity partly offset these effects. Bacterial community composition and methanotrophy genes did not vary with regional permafrost cover, and the latter changed similarly to methanogenesis with groundwater connectivity. Finally, we found an increase in sugar utilization genes in regions with less permafrost, which may further fuel methanogenesis. These results provide the microbial mechanism for observed increases in methane emissions associated with loss of permafrost cover in this region and suggest that future emissions will primarily be controlled by archaeal methanogens over methanotrophic bacteria as northern lakes warm. Our study more generally suggests that future predictions of aquatic carbon cycling will be improved by considering how climate warming exerts both direct effects associated with regional-scale permafrost thaw and indirect effects associated with local hydrology.     

Microbial biogeography of permafrost thaw ponds across the changing northern landscape

Microbial diversity varies at multiple spatial scales, but little is known about how climate change may influence this variation. Here we assessed the free‐living bacterioplankton composition of thaw ponds over a north‐south gradient of permafrost degradation in the eastern Canadian subarctic. Three nested spatial scales were compared: 1) among ponds within individual valleys 2) between two valleys within each landscape type, and 3) between landscape types (southern sporadic versus northern discontinuous permafrost). As a reference point, we sampled rock‐basin lakes whose formation was not related to permafrost thawing. β‐diversity was low at the smallest scale despite marked differences in limnological properties among neighboring ponds. β‐diversity was high among valleys, associated with greater environmental heterogeneity. The largest differences were between landscape types and appeared to reflect the concomitant effects of environmental filtering and dispersal limitation. Raup–Crick β‐diversity indicated that community assembly was driven by both stochastic (random extinction, dispersal, ecological drift) and deterministic (environmental filtering) processes. Communities sampled in the most degraded valley appeared primarily assembled through stochastic processes, while environmental filtering played a greater role at the other valleys. These results imply that climate warming and ongoing permafrost degradation will influence microbial community assembly, which in turn is likely to affect the functioning of thaw pond ecosystems.     

Thaw pond development and initial vegetation succession in experimental plots at a Siberian lowland tundra site

Background and aims

Permafrost degradation has the potential to change the Arctic tundra landscape. We observed rapid local thawing of ice-rich permafrost resulting in thaw pond formation, which was triggered by removal of the shrub cover in a field experiment. This study aimed to examine the rate of permafrost thaw and the initial vegetation succession after the permafrost collapse.

Methods

In the experiment, we measured changes in soil thaw depth, plant species cover and soil subsidence over nine years (2007–2015).

Results

After abrupt initial thaw, soil subsidence in the removal plots continued indicating further thawing of permafrost albeit at a much slower pace: 1 cm y^?1 over 2012–2015 vs. 5 cm y^?1 over 2007–2012. Grass cover strongly increased after the initial shrub removal, but later declined with ponding of water in the subsiding removal plots. Sedges established and expanded in the wetter removal plots. Thereby, the removal plots have become increasingly similar to nearby ‘natural’ thaw ponds.

Conclusions

The nine years of field observations in a unique shrub removal experiment at a Siberian tundra site document possible trajectories of small-scale permafrost collapse and the initial stage of vegetation recovery, which is essential knowledge for assessing future tundra landscape changes.

     

Biogeochemistry of organic carbon, CO2, CH4, and trace elements in thermokarst water bodies in discontinuous permafrost zones of Western Siberia

Active processes of permafrost thaw in Western Siberia increase the number of soil subsidencies, thermokarst lakes and thaw ponds. In continuous permafrost zones, this process promotes soil carbon mobilisation to water reservoirs, as well as organic matter (OM) biodegradation, which produces a permanent flux of carbon dioxide (CO₂) to the atmosphere. At the same time, the biogeochemical evolution of aquatic ecosystems situated in the transition zone between continuous permafrost and permafrost-free terrain remains poorly known. In order to better understand the biogeochemical processes that occur in thaw ponds and lakes located in discontinuous permafrost zones, we studied ~30 small (1–100,000 m²) shallow (<1 m depth) lakes and ponds formed as a result of permafrost subsidence and thaw of the palsa bog located in the transition zone between the tundra and forest-tundra (central part of Western Siberia). There is a significant increase in dissolved CO₂ and methane (CH₄) concentration with decreasing water body surface area, with the largest supersaturation with respect to atmospheric CO₂ and CH₄ in small (<100 m²) permafrost depressions filled with thaw water. Dissolved organic carbon (DOC), conductivity, and metal concentrations also progressively increase from large lakes to thaw ponds and depressions. As such, small water bodies with surface areas of 1–100 m² that are not accounted for in the existing lake and pond databases may significantly contribute to CO₂ and CH₄ fluxes to the atmosphere, as well as to the stocks of dissolved trace elements and organic carbon. In situ lake water incubation experiments yielded negligible primary productivity but significant oxygen consumption linked to the mineralisation rate of dissolved OM by heterotrophic bacterioplankton, which produce a net CO₂ flux to the atmosphere of 5 ± 2.5 mol C m² year^?1. The most significant result of this study, which has long-term consequences on our prediction of aquatic ecosystem development in the course of permafrost degradation is CO₂, CH₄, and DOC concentrations increase with decreasing lake age and size. As a consequence, upon future permafrost thaw, the increase in the number of small water bodies, accompanied by the drainage of large thermokarst lakes to the hydrological network, will likely favour (i) the increase of DOC and colloidal metal stocks in surface aquatic systems, and (ii) the enhancement of CO₂ and CH₄ fluxes from the water surface to the atmosphere. According to a conservative estimation that considers that the total area occupied by water bodies in Western Siberia will not change, this increase in stocks and fluxes could be as high as a factor of ten.     

Past vegetation dynamics of Vltavský luh, upper Vltava river valley in the Šumava mountains. Czech Republic

Six pollen diagrams from peat bogs in the Vltavsky luh (upper Vltava river valley) provide new information about vegetation reconstruction, woodland dynamics, and local development of mires during the Late-glacial and Holocene. Vegetation development began in the Oldest Dryas/B?ling with open park plant cover. In the Aller?d, woodland with Pinus and Betula developed, and in the Younger Dryas there was a steppe tundra with plants of open habitats. In the Pre-boreal, woodland tundra grew. In the Boreal, Corylus spread, and a major expansion of Picea began in the early Boreal. Picea spread during the Atlantic probably by two different migration routes. Fagus immigrated earlier than in the Bayerischer Wald and Oberpf?lzer Wald in the adjoining parts of Germany, and had its major expansion in the early Atlantic. Abies expanded in the late Atlantic. The great abundance of Abies in this area is remarkable, forming Abies or Abies-Fagus woods in less extreme habitats. Human occupation started in the Sub-boreal, as shown by both archaeology and palynology. However, human impact is recognized from anthropogenic indicators which appear in the early Atlantic. At the end of the later Sub-atlantic the development of natural woodland was interrupted by plantation of Picea according to historical and palynological evidence. Received November 13, 2000 / Accepted July 7, 2001     

Tundra be dammed: Beaver colonization of the Arctic

Increasing air temperatures are changing the arctic tundra biome. Permafrost is thawing, snow duration is decreasing, shrub vegetation is proliferating, and boreal wildlife is encroaching. Here we present evidence of the recent range expansion of North American beaver (Castor canadensis) into the Arctic, and consider how this ecosystem engineer might reshape the landscape, biodiversity, and ecosystem processes. We developed a remote sensing approach that maps formation and disappearance of ponds associated with beaver activity. Since 1999, 56 new beaver pond complexes were identified, indicating that beavers are colonizing a predominantly tundra region (18,293 km²) of northwest Alaska. It is unclear how improved tundra stream habitat, population rebound following overtrapping for furs, or other factors are contributing to beaver range expansion. We discuss rates and likely routes of tundra beaver colonization, as well as effects on permafrost, stream ice regimes, and freshwater and riparian habitat. Beaver ponds and associated hydrologic changes are thawing permafrost. Pond formation increases winter water temperatures in the pond and downstream, likely creating new and more varied aquatic habitat, but specific biological implications are unknown. Beavers create dynamic wetlands and are agents of disturbance that may enhance ecosystem responses to warming in the Arctic.     

Permafrost conditions in peatlands regulate magnitude,timing, and chemical composition of catchment dissolved organic carbon export

Permafrost thaw in peatlands has the potential to alter catchment export of dissolved organic carbon (DOC) and thus influence downstream aquatic C cycling. Subarctic peatlands are often mosaics of different peatland types, where permafrost conditions regulate the hydrological setting of each type. We show that hydrological setting is key to observed differences in magnitude, timing, and chemical composition of DOC export between permafrost and nonpermafrost peatland types, and that these differences influence the export of DOC of larger catchments even when peatlands are minor catchment components. In many aspects, DOC export from a studied peatland permafrost plateau was similar to that of a forested upland catchment. Similarities included low annual export (2–3 g C m^?2) dominated by the snow melt period (~70%), and how substantial DOC export following storms required wet antecedent conditions. Conversely, nonpermafrost fens had higher DOC export (7 g C m^?2), resulting from sustained hydrological connectivity during summer. Chemical composition of catchment DOC export arose from the mixing of highly aromatic DOC from organic soils from permafrost plateau soil water and upland forest surface horizons with nonaromatic DOC from mineral soil groundwater, but was further modulated by fens. Increasing aromaticity from fen inflow to outlet was substantial and depended on both water residence time and water temperature. The role of fens as catchment biogeochemical hotspots was further emphasized by their capacity for sulfate retention. As a result of fen characteristics, a 4% fen cover in a mixed catchment was responsible for 34% higher DOC export, 50% higher DOC concentrations and ~10% higher DOC aromaticity at the catchment outlet during summer compared to a nonpeatland upland catchment. Expansion of fens due to thaw thus has potential to influence landscape C cycling by increasing fen capacity to act as biogeochemical hotspots, amplifying aquatic C cycling, and increasing catchment DOC export.     

Local and Landscape Factors Driving the Structure of Tropical Anuran Communities: Do Ephemeral Ponds have a Nested Pattern?

The sets of species in animal and plant communities often comprise nested subsets of the species in broader communities. Although most mechanisms causing nested patterns are known and have been demonstrated for different environments and taxa, how amphibian communities are structured in ephemeral ponds in tropical disturbed landscapes remains unknown. We investigated if pond size, duration, presence of trees (local factors), and the proportion of forest cover surrounding ponds (landscape factor) affect anuran species richness and composition, and if pond assemblages showed a nested pattern. We sampled 11 ephemeral ponds in a pasture matrix near a large Atlantic Forest remnant in Brazil and measured local and landscape variables inside two buffer zones around each pond (100 and 500 m). We marked 1514 individuals from 23 anuran species, and found that richness in ponds ranged from 3–14 species. Both local and landscape factors explained frog species richness in the sampled ponds, and seemed to affect community composition. Frog communities occurred in a non‐nested pattern, contrary to our expectations: species found in poor subsets were not found in larger, more complex ponds. Local and landscape characteristics create a variety of environments in ephemeral ponds, even in impoverished ones; these characteristics restrict pond occupancy for some species, and result in a non‐nested pattern.     

The interplay between local and landscape scales on the density of pond-dwelling anurans in subtropical grasslands

We investigated the role of local and landscape environmental variables on anurans density classified as habitat specialists and generalists in grassland landscapes, known as South Brazilian grasslands (SBG). In this region, we surveyed 187 ponds distributed over 40 landscape sampling units. For each pond, 31 local environmental variables were measured. Each landscape sampling unit was embedded within a larger regional sampling unit with different landscape properties. For each landscape and regional sampling units, 16 landscape metrics were extracted from a land cover and use map. We recorded 35 species, eleven of which are specialists in the SBG. The specialists were affected by 11 local and 2 landscape environmental variables, while generalists were affected by 14 local and one landscape environmental variable. Thus, specialists and generalists presented different relationships with local and landscape variables, but in general local variables had a greater influence on the density of anurans than the landscape variables. However, the landscape indirectly influenced local variables because higher quality ponds were in landscapes with higher percentages of natural habitat. In conclusion, reproductive sites with higher local quality and located within landscapes with higher percentages of natural grasslands are essential to conserve anurans in this habitat. Effective conservation of such sites would benefit from further studies that assess effects of land use and biotic integrity of ponds, which can help to determine (a) the relative effects of local habitat quality of ponds and (b) the effectiveness of protecting ponds and their local surroundings for anuran conservation in SBG. Abstract in Portuguese is available with online material.     

Lagoonal stormwater detention ponds as promoters of harmful algal blooms and eutrophication along the South Carolina coast

In the rapidly urbanizing coastal zone of South Carolina, intensive landscape maintenance and turf management are significant sources of nonpoint source pollutant loadings. The best management practice of choice for stormwater in this region is wet detention ponds, the majority of which are brackish lagoons. Typically, stormwater is piped directly into the ponds, but ponds have limited capacity for processing pollutants. These eutrophic brackish ponds are “hot spots” for harmful algal blooms (HABs)—over 200 blooms from 23 different species were documented over the last 4 years, many associated with measured toxins, fish kills or shellfish health problems. Because these ponds exchange with tidal creeks, they are potential sources for HAB dispersion into adjacent estuaries. Also, flux measurements indicated that groundwater was both a source of nutrients to the ponds and a mechanism for transporting nutrients from the ponds. These findings suggest that manmade ponds as presently designed along the SC coast may contribute to estuarine eutrophication and HAB prevalence. A summary of HAB occurrences in SC lagoonal ponds from 2001 to 2005 is presented, and a project is described that simulates the effectiveness of constructed wetlands as a supplementary best management practice designed to process stormwater and groundwater and remove nutrients prior to entering wet detention ponds.     

农业景观中环境因素对两栖类生物分布的影响

以黄河下游地区封丘县为研究区,在地理信息系统和R软件的支持下,在栖息地水平和景观水平上,分析了两栖类生物分布与栖息地变量(池塘水体溶解氧DO、电导率COND、浊度TURB、水体氨氮NH₃-N、池塘内植被盖度VEG_interior、池塘内挺水植物盖度EMER、池塘边缘植被盖度VEG_edge、两栖类幼虫捕食者PRE和池塘面积AREA)和采样点池塘250、500、1000、2000 m半径缓冲区内景观变量(池塘面积AP、与最近道路的距离DR、耕地面积AF、林地面积AW、Shannon多样性指数SHDI和蔓延度指数CONTAG)的关系.结果表明: 中华大蟾蜍的分布主要与栖息地变量中的PRE和较大缓冲区半径内的景观变量(AW2000、DR2000、SHDI1000、CONTAG1000)相关;黑斑侧褶蛙的分布与栖息地变量中的EMER和较小缓冲区半径内的景观变量(SHDI500)关系密切;金线侧褶蛙的分布主要与栖息地变量中的VEG_interior和PRE相关;泽陆蛙的分布主要与较大缓冲区半径内的景观变量(AF2000、SHDI2000)相关;两栖类生物总体上主要与栖息地变量中的EMER和较小缓冲区半径内的景观变量(SHDI500)相关.在农业景观中,保护两栖类生物应该保护永久性和半永久性池塘、提高池塘内部植被盖度、增强栖息地池塘之间的功能连通性.     

Nationwide groundwater surveillance of noroviruses in South Korea, 2008

To inspect the norovirus contamination of groundwater in South Korea, a nationwide study was performed in the summer (June to August) and winter (October to December) of 2008. Three-hundred sites designated by the government ministry were inspected. Water samples were collected for analysis of water quality, microorganism content, and viral content. Water quality was assessed by temperature, pH, turbidity, residual chlorine, and nitrite nitrogen content. Microorganism contents were analyzed bacteria, total coliforms, Escherichia coli, and bacteriophage. Virus analyses included panenterovirus and norovirus. Two primer sets were used for the detection of norovirus genotypes GI and GII, respectively. Of 300 samples, 65 (21.7%) were norovirus positive in the summer and in 52 (17.3%) were norovirus positive in the winter. The genogroup GI noroviruses that were identified were GI-1, GI-2, GI-3, GI-4, GI-5, GI-6, and GI-8 genotypes; those in the GII genogroup were GII-4 and GII-Yuri genotypes. The analytic data showed correlative relationships between the norovirus detection rate and the following parameters: water temperature and turbidity in physical-chemical parameters and somatic phage in microbial parameters. It is necessary to periodically monitor waterborne viruses that frequently cause epidemic food poisoning in South Korea for better public health and sanitary conditions.     

Postglacial history of New Zealand wetlands and implications for their conservation

Most New Zealand wetlands formed at or after the end of the last glaciation (c.?18?000 cal yrs BP). Those associated with major rivers and close to the coast tend to be young as erosive processes both destroy and initiate wetlands. However, there is a strong linear trend in initiations since 14?000 cal yrs BP, which suggests that geomorphic processes such as soil deterioration, landslides, sand dune movement and river course changes are constantly adding new, permanent wetlands. Most wetlands began as herbaceous fens but usually transitioned to shrub- or forest-covered bog?fen systems, in particular after the beginning of the Holocene (11?500 cal yrs BP). Raised bogs formed from fens during the late-glacial and early Holocene, when river down-cutting isolated them from groundwater inflow. As climates warmed through the late-glacial and early Holocene, wooded wetlands spread and over 75% of lowland peat profiles preserve wood layers. Large basins with high water inflow often contain lakes or lagoons and have maintained herbaceous swamps, whereas those with limited catchments have become almost entirely covered with forest or shrub. Wetlands in drier districts tend to have been initiated during the mid- and late Holocene as the climate cooled and rain-bearing systems penetrated more often. Ombrogenous montane and alpine bogs may have been initiated by the same climate change. Natural fires frequently burnt some wetlands, particularly within the vast bog complexes of the Waikato Basin, but many wetlands record occasional fire episodes. By the time M?ori arrived in the 13th century, about 1% of the landscape was covered with some form of wetland and most of that wetland was under woody cover. M?ori firing of the landscape began the process of removing the woody cover, which induced wetter, more herbaceous systems and initiated new wetlands. Deforestation of catchments in drier districts increased water yield that may in turn have created lowland fens and lagoons. European logging, fire and draining destroyed both pristine forested wetlands and fire-transformed systems from the M?ori settlement era. The loss of wetlands is now largely a crisis of continued degradation through draining, weed invasion and fire in already human-altered systems in productive landscapes. Wetland history can help assess values and inform goals for conservation of wetlands, but transformation of the lowland landscape has been so complete that an historically authentic endpoint is unrealistic for most wetlands. The major conservation emphasis should be on larger wetlands that provide a range of ecosystem services.     

Bacterial communities and greenhouse gas emissions of shallow ponds in the High Arctic

Permafrost thawing in lowland Arctic tundra results in a polygonal patterned landscape and the formation of numerous small ponds. These ponds emit biologically mediated carbon dioxide (CO₂) and methane (CH₄). Their greenhouse gas (GHG) emissions are variable, for reasons that are not well understood. Emissions are related to a balance between GHG producers and consumers, as well as to physical properties of the water column controlling gas exchange rates with the atmosphere. Here, we investigated the bacterial diversity of polygonal and runnel ponds, two geomorphologically distinct pond types commonly found in continuous permafrost regions. Using a combination of 16S rRNA Sanger sequencing and high-throughput amplicon sequencing, we found that bacterial communities in overlying waters were clearly dominated by carbon degraders and were similar in both pond types, despite their variable physical and chemical properties. However, surface sediment communities in the two pond types were significantly different. Polygonal pond sediment was colonized by carbon degraders (46–29 %), cyanobacteria (20–27 %) that take up CO₂ and produce oxygen, and methanotrophs (11–20 %) that consume CH₄ and require oxygen. In contrast, cyanobacteria were effectively absent from the surface sediment of runnel ponds, which in addition to carbon degraders (65–81 %), were colonized by purple non-sulfur bacteria (5–21 %), and by fewer methanotrophs (1–5 %). The link between the methanotrophic community and the type of ponds could potentially be used to improve upscale estimates of GHG emissions based on landscape morphology in such remote regions.     

Contrasting responses of phytoplankton and benthic algae to recent nutrient enrichment in Arctic tundra ponds

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Thermokarst rates intensify due to climate change and forest fragmentation in an Alaskan boreal forest lowland

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Carbon accumulation in a permafrost polygon peatland: steady long‐term rates in spite of shifts between dry and wet conditions

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