Viral Activity in Two Contrasting Lake Ecosystems

For aquatic systems, especially freshwaters, there is little data on the long-term (i.e., >6-month period) and depth-related variability of viruses. In this study, we examined virus-induced mortality of heterotrophic bacteria over a 10-month period and throughout the water column in two lakes of the French Massif Central, the oligomesotrophic Lake Pavin and the eutrophic Lake Aydat. Concurrently, we estimated nonviral mortality through heterotrophic nanoflagellate and ciliate bacterivory. Overall, viral infection parameters were much less variable than bacterial production. We found that the frequency of visibly infected cells (FVIC), estimated using transmission electron microscopy, peaked in both lakes at the end of spring (May to June) and in early autumn (September to October). FVIC values were significantly higher in Lake Pavin (mean [M] = 1.6%) than in Lake Aydat (M = 1.1%), whereas the opposite trend was observed for burst sizes, which averaged 25.7 and 30.2 virus particles bacterium⁻¹, respectively. We detected no significant depth-related differences in FVIC or burst size. We found that in both lakes the removal of bacterial production by flagellate grazing (M_Pavin = 37.7%, M_Aydat = 18.5%) was nearly always more than the production removed by viral lysis (M_Pavin = 16.2%, M_Aydat = 19%) or ciliate grazing (M_Pavin = 2.7%, M_Aydat = 8.8%). However, at specific times and locations, viral lysis prevailed over protistan grazing, for example, in the anoxic hypolimnion of Lake Aydat. In addition, viral mortality represented a relatively constant mortality source in a bacterial community showing large variations in growth rate and subject to large variations in loss rates from grazers. Finally, although viruses did not represent the main agent of bacterial mortality, our data seem to show that their relative importance was higher in the less productive system.     

Methane Biogeochemistry and Methanogen Communities in Two Northern Peatland Ecosystems,New York State

Rates of methane (CH₄) production vary considerably among northern peat-forming wetlands, and it is not clear whether variability is caused by environmental factors affecting CH₄ production or differences in methanogen communities. We investigated CH₄ production and emission dynamics concomitantly with 16S rRNA gene sequence-based community analysis of Archaea in two contrasting peat-forming northern wetlands, an ombrotrophic bog and a minerotrophic conifer swamp. Individual measurements of CH₄ emissions to the atmosphere followed a lognormal distribution pattern in both sites, and mean rates were 30× greater in the bog site. Rates of CH₄ production measured in vitro were initially 3× greater in the bog than in the conifer swamp; although, after 30 days of incubation, production rates were similar suggesting that in situ environmental conditions limited production in the conifer swamp. Amplified ribosomal DNA restriction analysis (ARDRA) and rarefaction techniques indicated that both sites had similar levels of archaeal richness, with 27 unique taxa in the bog and 23 taxa in the conifer swamp. However, the bog had more pronounced dominance of a few taxa, whereas the conifer swamp had more even distribution among taxa. A 16S rRNA gene sequence-based phylogenetic analysis indicated high levels of diversity with similarity to known methanogenic families Methanosarcinaceae, Methanosaetaceae, Methanobacteriaceae, and likely Methanomicrobiaceae as well as two additional lineages previously characterized as groups of yet uncultivated Euryarchaeota commonly occurring in flooded rice soils. Therefore, sites with low and high rates of CH₄ production supported very diverse methanogenic communities.     

Contrasting genetic structures in sister species of North American scrub-jays

Threatened Florida scrub-jays (Aphelocoma coerulescens breed communally, are restricted to xeric sandy scrub habitat, generally disperse fewer than three territory diameters. Closely related Western scrub-jays (A. californica) do not breed communally, have a broader habitat range, disperse greater distances, and are not threatened. We compared the genetic structure of 445 individuals in 11 populations in Florida with 157 individuals in eight populations of Western scrub-jays. At ten microsatellite loci, Florida had 24 out of 47 total alleles, while Western scrub-jays had 44. The Florida populations were more differentiated (G_ST = 0.048) than were a set of five California populations (G_ST = 0.015). A randomization extension of a Mantel test showed a stronger correlation between geographic and Cavalli-Sforza genetic distances among Western than Florida populations. Neighbour-joining trees clustered Florida populations from the same sandy ridge systems, suggesting that habitat continuity is more important than geographic proximity in allowing gene flow and preventing differentiation. For Western populations, isolation by distance appears to be the major determinant of genetic structure. Our results suggest that contrasting genetic structures may arise between closely related species, as a result of differences in ecology and social system. Conserving extant genetic variation in Florida jays will require maintaining viable populations in each of the major sandy ridge systems.     

Controls on Microbial Production of Methane and Carbon Dioxide in Three Sphagnum-Dominated Peatland Ecosystems as Revealed by a Reciprocal Field Peat Transplant Experiment

We examined controls on mineralization of carbon to methane (CH₄) and carbon dioxide (CO₂) in Sphagnum (moss)-dominated peatland ecosystems by transplanting surface (5 cm deep) and subsurface (40 cm deep) peat samples reciprocally among three sites for periods ranging from 4 to 25 months. The sites were Big Run Bog in West Virginia, USA, Bog Lake Bog in Minnesota, USA, and Bog 307 in Ontario, Canada. Immediately upon retrieval, we incubated the peat samples in the laboratory at 12 and 22°C under both anoxic and oxic conditions to estimate rates of carbon mineralization. Transplanting affected surface peat more than subsurface peat. Peat incubated within Bog Lake Bog in Minnesota had the highest rates of CH₄ production, regardless of origin, whereas transplanting did not affect rates of CO₂ production measured concomitantly. Peat that originated in Big Run Bog in West Virginia generally maintained higher rates of CH₄ production and CO₂ production than peat from the other two sites after incubation in the field. The temperature dependence (Q ₁₀) of CH₄ production and CO₂ production varied among transplant sites, but not among peat origins, suggesting physiological adaptations of microbial communities to local environmental conditions. Differences in organic matter quality of the peat, particularly lignin chemistry, helped explain the results: (a) CH₄ production correlated with fresher lignin derived from Carex sedges, and (b) CO₂ production correlated with woody lignin. We concluded that, although both site conditions (climate, nutrient status, and microbial communities) and organic matter quality influence carbon mineralization in peat, interactive effects occur and may differ depending on peat temperature. Moreover, CH₄ production and CO₂ production respond differently to environmental regulators.     

Controls on Soil Organic Carbon Stocks and Turnover Among North American Ecosystems

Despite efforts to understand the factors that determine soil organic carbon (SOC) stocks in terrestrial ecosystems, there remains little information on how SOC turnover time varies among ecosystems, and how SOC turnover time and C input, via plant production, differentially contribute to regional patterns of SOC stocks. In this study, we determined SOC stocks (gC m⁻²) and used soil radiocarbon measurements to derive mean SOC turnover time (years) for 0–10 cm mineral soil at ten sites across North America that included arctic tundra, northern boreal, northern and southern hardwood, subtropical, and tropical forests, tallgrass and shortgrass prairie, mountain grassland, and desert. SOC turnover time ranged 36-fold among ecosystems, and was much longer for cold tundra and northern boreal forest and dry desert (1277–2151 years) compared to other warmer and wetter habitats (59–353 years). Two measures of C input, net aboveground production (NAP), determined from the literature, and a radiocarbon-derived measure of C flowing to the 0–10 cm mineral pool, I, were positively and SOC turnover time was negatively associated with mean annual evapotranspiration (ET) among ecosystems. The best fit model generated from the independent variables NAP, I, annual mean temperature and precipitation, ET, and clay content revealed that SOC stock was best explained by the single variable I. Overall, these findings indicate the primary role that C input and the secondary role that C stabilization play in determining SOC stocks at large regional spatial scales and highlight the large vulnerability of the global SOC pool to climate change.     

Spatial Variation in Soil Properties among North American Ecosystems and Guidelines for Sampling Designs

Soils are highly variable at many spatial scales, which makes designing studies to accurately estimate the mean value of soil properties across space challenging. The spatial correlation structure is critical to develop robust sampling strategies (e.g., sample size and sample spacing). Current guidelines for designing studies recommend conducting preliminary investigation(s) to characterize this structure, but are rarely followed and sampling designs are often defined by logistics rather than quantitative considerations. The spatial variability of soils was assessed across ∼1 ha at 60 sites. Sites were chosen to represent key US ecosystems as part of a scaling strategy deployed by the National Ecological Observatory Network. We measured soil temperature (T_s) and water content (SWC) because these properties mediate biological/biogeochemical processes below- and above-ground, and quantified spatial variability using semivariograms to estimate spatial correlation. We developed quantitative guidelines to inform sample size and sample spacing for future soil studies, e.g., 20 samples were sufficient to measure T_s to within 10% of the mean with 90% confidence at every temperate and sub-tropical site during the growing season, whereas an order of magnitude more samples were needed to meet this accuracy at some high-latitude sites. SWC was significantly more variable than T_s at most sites, resulting in at least 10× more SWC samples needed to meet the same accuracy requirement. Previous studies investigated the relationship between the mean and variability (i.e., sill) of SWC across space at individual sites across time and have often (but not always) observed the variance or standard deviation peaking at intermediate values of SWC and decreasing at low and high SWC. Finally, we quantified how far apart samples must be spaced to be statistically independent. Semivariance structures from 10 of the 12-dominant soil orders across the US were estimated, advancing our continental-scale understanding of soil behavior.     

Pathways for Methanogenesis and Diversity of Methanogenic Archaea in Three Boreal Peatland Ecosystems

The main objectives of this study were to uncover the pathways used for methanogenesis in three different boreal peatland ecosystems and to describe the methanogenic populations involved. The mesotrophic fen had the lowest proportion of CH₄ produced from H₂-CO₂. The oligotrophic fen was the most hydrogenotrophic, followed by the ombrotrophic bog. Each site was characterized by a specific group of methanogenic sequences belonging to Methanosaeta spp. (mesotrophic fen), rice cluster-I (oligotrophic fen), and fen cluster (ombrotrophic bog).     

Litter Decomposition in Temperate Peatland Ecosystems: The Effect of Substrate and Site

Abstract The large accumulation of organic matter in peatlands is primarily caused by slow rates of litter decomposition. We determined rates of decomposition of major peat-forming litters of vascular plants and mosses at five sites: a poor fen in New Hampshire and a bog hummock, a poor fen, a beaver pond margin and a beaver pond in Ontario. We used the litterbag technique, retrieving triplicate litterbags six or seven times over 3–5 years, and found that simple exponential decay and continuous-quality non-linear regression models could adequately characterize the decomposition in most cases. Within each site, the rate of decomposition at the surface was generally Typha latifolia leaves = Chamaedaphne calyculata leaves = Carex leaves > Chamaedaphne calyculata stems > hummock Sphagnum = lawn/hollow Sphagnum, with exponential decay constant (k) values generally ranging from 0.05 to 0.37 and continuous-quality model initial quality (q ₀ ) values ranging from 1.0 (arbitrarily set for Typha leaves) to 0.7 (Sphagnum). In general, surface decay rates were slowest at the bog hummock site, which had the lowest water table, and in the beaver pond, which was inundated, and fastest at the fens. The continuous-quality model site decomposition parameter (u ₀ ) ranged from 0.80 to 0.17. Analysis of original litter samples for carbon, nitrogen and proximate fractions revealed a relatively poor explanation of decomposition rates, as defined by k and q ₀ , compared to most well-drained ecosystems. Three litters, roots of sedge and a shrub and Typha leaves, were placed at depths of 10, 30 and 60 cm at the sites. Decomposition rates decreased with depth at each site, with k means of 0.15, 0.08 and 0.05 y⁻¹ at 10, 30 and 60 cm, respectively, and u ₀ of 0.25, 0.13 and 0.07. These differences are primarily related to the position of the water table at each site and to a lesser extent the cooler temperatures in the lower layers of the peat. The distinction between bog and fen was less important than the position of the water table. These results show that we can characterize decomposition rates of surface litter in northern peatlands, but given the large primary productivity below-ground in these ecosystems, and the differential rates of decomposition with depth, subsurface input and decomposition of organic matter is an important and relatively uncertain attribute.     

Environmental Controls of Cryptogam Composition and Diversity in Anthropogenic and Natural Peatland Ecosystems of Chilean Patagonia

Peatlands exhibit highly characteristic ecological traits and are unique complex ecosystems. Nevertheless, knowledge about southern South American peatlands is very limited. In this study, we analyzed species composition of bryophytes and lichens of Southern Hemisphere peatlands, specifically from eight peatlands of Isla Grande de Chiloé (Chiloé Island) in southern Chile (42°–43°S and 75°–73°W). Two kinds of Sphagnum peatlands were studied: natural and anthropogenic peatlands. Our results indicate the existence of clear environmental gradients affecting the structure of bryo-lichenic communities in the Sphagnum peatlands of Chiloé. Canonical correspondence analysis suggests that variation in bryophyte and lichen species composition mainly follows ombrotrophic–minerotrophic and lithotrophic-thalassotrophic gradients. Surface-water chemistry is the most significant factor accounting for changes in floristic composition among our study sites. In contrast to our expectations, bog origin (natural or anthropic) was not the most significant factor accounting for changes in floristic composition among peatlands. Other elements, such as the water source supplying peatlands or the influence of sea spray, were more relevant in the bryo-lichenic flora species occurrence in the peatlands of Chiloé. We also observed clear differences in ecological niches among species in general additive model response curves. Therefore, our results show that despite the origin, the ecology of peatlands follows common rules with peatlands from the Northern Hemisphere.     

The Carbon Balance of Two Contrasting Mountain Forest Ecosystems in Switzerland: Similar Annual Trends,but Seasonal Differences

Net ecosystem exchange (NEE) of two contrasting mountain forest types in Switzerland was measured by eddy covariance (EC) measurements at a montane mixed forest, the Lägeren forest, over 5 years (2005–2009), and at a subalpine coniferous forest, the Seehornwald in Davos, over 12 years (1997–2009). NEE was validated against annual carbon (C) storage estimates, based on biometric and soil respiration measurements as well as soil C modeling. Three different approaches were used: (1) calculation of net ecosystem production by quantifying C pools and fluxes, (2) assessment of change in wood biomass and soil C storage (ΔC), and (3) application of biomass expansion factors. Although biometric estimates were sensitive to assumptions made for each method applied, they agreed well with measured NEE. Comparing 5 years of EC measurements available at both sites during 2005 and 2009 revealed that NEE, gross primary production (GPP), and total ecosystem respiration (TER) were larger at the Lägeren forest compared to the Davos forest, whereas soil respiration and soil C sequestration were of similar magnitudes. Both sites showed similar annual trends for NEE, GPP and TER, but different seasonal courses, due to different responses to environmental conditions (temperature, soil moisture, and radiation). Differences in the magnitude as well as in the seasonality of ecosystem CO₂ exchange could mainly be attributed to tree phenology, productivity, and carbon allocation patterns, which are combined effects of tree type (broad-leaved vs. coniferous trees) and site-specific climatic conditions. Flux differences between the two mountain sites highlight the importance of considering the role of altitude in ecological studies and modeling.     

Contrasting changes in the abundance and diversity of North American bird assemblages from 1971 to 2010

Although it is generally recognized that global biodiversity is declining, few studies have examined long‐term changes in multiple biodiversity dimensions simultaneously. In this study, we quantified and compared temporal changes in the abundance, taxonomic diversity, functional diversity, and phylogenetic diversity of bird assemblages, using roadside monitoring data of the North American Breeding Bird Survey from 1971 to 2010. We calculated 12 abundance and diversity metrics based on 5‐year average abundances of 519 species for each of 768 monitoring routes. We did this for all bird species together as well as for four subgroups based on breeding habitat affinity (grassland, woodland, wetland, and shrubland breeders). The majority of the biodiversity metrics increased or remained constant over the study period, whereas the overall abundance of birds showed a pronounced decrease, primarily driven by declines of the most abundant species. These results highlight how stable or even increasing metrics of taxonomic, functional, or phylogenetic diversity may occur in parallel with substantial losses of individuals. We further found that patterns of change differed among the species subgroups, with both abundance and diversity increasing for woodland birds and decreasing for grassland breeders. The contrasting changes between abundance and diversity and among the breeding habitat groups underscore the relevance of a multifaceted approach to measuring biodiversity change. Our findings further stress the importance of monitoring the overall abundance of individuals in addition to metrics of taxonomic, functional, or phylogenetic diversity, thus confirming the importance of population abundance as an essential biodiversity variable.     

Functional Convergence of Ecosystems: Evidence from Body Mass Distributions of North American Late Miocene Mammal Faunas

There is disagreement among ecologists as to whether ecosystem system behavior in general is the net result of all of the complex internal system interactions (bottom-driven) or if the behavior is driven by a limited number of key processes (top-driven). If ecosystems are primarily bottom-driven in nature, then it is unlikely that any two complex ecosystems will ever behaviorally converge as a simple matter of probability, or that their behaviors will ever be predictable. Conversely, evidence of ecosystem convergence would suggest that the systems are top-driven, with the corollary that their behaviors can be understood (and therefore in principle predicted) without a complete understanding of their internal workings. Research has demonstrated that body mass distributions of terrestrial animals broadly reflect ecosystem function. Thus, comparable but causally disconnected terrestrial ecosystems that demonstrate similar body mass distributions would suggest ecosystem convergence. To look for this possible convergence, I generated body mass distributions in a time series for late Miocene North American mammal faunas from the Gulf Coastal Plains, Great Plains, and Pacific coastal region, and compared them with data from the modern Serengeti savanna region. The data show that during the early late Miocene Gulf Coastal Plain faunas resembled each other but were distinctly different from that of the Serengeti, the Great Plains fauna resembled the Serengeti, while the Pacific Coast fauna showed no resemblance to any of the others. However, during the latest Miocene the Gulf Coastal Plain faunas were transformed so as to strongly resemble the Serengeti fauna. The resemblance with the Serengeti was maintained by the Great Plains faunas until at least the end of the Miocene, while the Pacific Coast faunas remained distinctly different from the others. These findings suggest that the late Miocene ecosystems of the Gulf Coastal Plain and Great Plains regions (but not the Pacific Coast region) converged with that of the Serengeti savanna fauna and thus that these ecosystems were/are top-driven rather than bottom-driven in nature.     

Plant Species Composition Can Be Used as a Proxy to Predict Methane Emissions in Peatland Ecosystems After Land-Use Changes

Land-use change in peatlands affects important drivers of CH₄ emission such as groundwater level and nutrient availability. Due to the high spatial and temporal variability of such environmental drivers, it is hard to make good predictions of CH₄ emissions in the context of land-use changes. Here, we used plant species composition as a stable integrator of environmental drivers of CH₄ emissions. We used weighted averaging regression and calibration to make a direct link between plant species composition and CH₄ flux in an effort to predict values of CH₄ emission for a land-use gradient in two extensive peatland sites. Our predicted CH₄ emissions showed good fit with observed values. Additionally, we showed that a quick characterization of vegetation composition, by the dominant species only, provides equally good predictions of CH₄ emissions. The use of mean groundwater level alone for predicting emissions showed the same predictive power as our models. However, water level showed strong variability in time. Furthermore, the inverse relationship between water level and CH₄ emission can lead to higher errors in predictions at sites with higher CH₄ emission. The performance of our model was comparable with those of mechanistic models developed for natural wetland ecosystems. However, such mechanistic models require complex input parameters that are rarely available. We propose the use of plant species composition as a simple and effective alternative for deriving predictions of CH₄ emissions in peatlands in the context of land-use change.     

Contrasting long-term alpine and subalpine precipitation trends in a mid-latitude North American mountain system,Colorado Front Range,USA

Background: Long-term climate trends in mountain systems often vary strongly with elevation.

Aims: To evaluate elevation dependence in long-term precipitation trends in subalpine forest and alpine tundra zones of a mid-continental, mid-latitude North American mountain system and to relate such dependence to atmospheric circulation patterns.

Methods: We contrasted 59-year (1952–2010) precipitation records of two high-elevation climate stations on Niwot Ridge, Colorado Front Range, Rocky Mountains, USA. The sites, one in forest (3022 m a.s.l.) and the other in alpine tundra (3739 m), are closely located (within 7 km horizontally, ca. 700 m vertically), but differ with respect to proximity to the mountain-system crest (the Continental Divide).

Results: The sites exhibited significant differences in annual and seasonal precipitation trends, which depended strongly on their elevation and distance from the Continental Divide. Annual precipitation increased by 60 mm (+6%) per decade at the alpine site, with no significant change at the subalpine site. Seasonally, trends at the alpine site were dominated by increases in winter, which we suggest resulted from an increase in orographically generated precipitation over the Divide, driven by upper-air (700 hPa) north-westerly flow. Such a change was not evident at the subalpine site, which is less affected by orographic precipitation on north-westerly flow.

Conclusions: Elevation dependence in precipitation trends appears to have arisen from a change in upper-air flow from predominantly south-westerly to north-westerly. Dependence of precipitation trends on topographic position and season has complex implications for the ecology and hydrology of Niwot Ridge and adjacent watersheds, involving interactions among physical processes (e.g. snowpack dynamics) and biotic responses (e.g. in phenologies and ecosystem productivity).     

Evolutionary Strategies of Viruses,Bacteria and Archaea in Hydrothermal Vent Ecosystems Revealed through Metagenomics

The deep-sea hydrothermal vent habitat hosts a diverse community of archaea and bacteria that withstand extreme fluctuations in environmental conditions. Abundant viruses in these systems, a high proportion of which are lysogenic, must also withstand these environmental extremes. Here, we explore the evolutionary strategies of both microorganisms and viruses in hydrothermal systems through comparative analysis of a cellular and viral metagenome, collected by size fractionation of high temperature fluids from a diffuse flow hydrothermal vent. We detected a high enrichment of mobile elements and proviruses in the cellular fraction relative to microorganisms in other environments. We observed a relatively high abundance of genes related to energy metabolism as well as cofactors and vitamins in the viral fraction compared to the cellular fraction, which suggest encoding of auxiliary metabolic genes on viral genomes. Moreover, the observation of stronger purifying selection in the viral versus cellular gene pool suggests viral strategies that promote prolonged host integration. Our results demonstrate that there is great potential for hydrothermal vent viruses to integrate into hosts, facilitate horizontal gene transfer, and express or transfer genes that manipulate the hosts’ functional capabilities.