The biological controls of soil carbon accumulation following wildfire and harvest in boreal forests: A review.

Boreal forests are frequently subjected to disturbances, including wildfire and clear-cutting. While these disturbances can cause soil carbon (C) losses, the long-term accumulation dynamics of soil C stocks during subsequent stand development is controlled by biological processes related to the balance of net primary production (NPP) and outputs via heterotrophic respiration and leaching, many of which remain poorly understood. We review the biological processes suggested to influence soil C accumulation in boreal forests. Our review indicates that median C accumulation rates following wildfire and clear-cutting are similar (0.15 and 0.20 Mg ha-1 year-1, respectively), however, variation between studies is extremely high. Further, while many individual studies show linear increases in soil C stocks through time after disturbance, there are indications that C stock recovery is fastest early to mid-succession (e.g. 15-80 years) and then slows as forests mature (e.g. >100 years). We indicate that the rapid build-up of soil C in younger stands appears not only driven by higher plant production, but also by a high rate of mycorrhizal hyphal production, and mycorrhizal suppression of saprotrophs. As stands mature, the balance between reductions in plant and mycorrhizal production, increasing plant litter recalcitrance, and ectomycorrhizal decomposers and saprotrophs have been highlighted as key controls on soil C accumulation rates. While some of these controls appear well understood (e.g. temporal patterns in NPP, changes in aboveground litter quality), many others remain research frontiers. Notably, very little data exists describing and comparing successional patterns of root production, mycorrhizal functional traits, mycorrhizal-saprotroph interactions, or C outputs via heterotrophic respiration and dissolved organic C following different disturbances. We argue that these less frequently described controls require attention, as they will be key not only for understanding ecosystem C balances, but also for representing these dynamics more accurately in soil organic C and Earth system models.

Comparison of the seasonal and successional variation of asymbiotic and symbiotic nitrogen fixation along a glacial retreat chronosequence.

Climate change is resulting in accelerated retreat of glaciers worldwide and much nitrogen-poor debris is left after glacier retreats. Asymbiotic dinitrogen (N2) fixation (ANF) can be considered a 'hidden' source of nitrogen (N) for non-nodulating plants in N limited environments; however, seasonal variation and its relative importance in ecosystem N budgets, especially when compared with nodulating symbiotic N2-fixation (SNF), is not well-understood. In this study, seasonal and successional variations in nodulating SNF and non-nodulating ANF rates (nitrogenase activity) were compared along a glacial retreat chronosequence on the eastern edge of the Tibetan Plateau. Key factors regulating the N2-fixation rates as well as the contribution of ANF and SNF to ecosystem N budget were also examined. Significantly greater nitrogenase activity was observed in nodulating species (0.4-17,820.8 nmol C2H4 g-1 d-1) compared to non-nodulating species (0.0-9.9 nmol C2H4 g-1 d-1) and both peaked in June or July. Seasonal variation in acetylene reduction activity (ARA) rate in plant nodules (nodulating species) and roots (non-nodulating species) was correlated with soil temperature and moisture while ARA in non-nodulating leaves and twigs was correlated with air temperature and humidity. Stand age was not found to be a significant determinant of ARA rates in nodulating or non-nodulating plants. ANF and SNF contributed 0.3-51.5 % and 10.1-77.8 %, respectively, of total ecosystem N input in the successional chronosequence. In this instance, ANF exhibited an increasing trend with successional age while SNF increased only at stages younger than 29 yr and then decreased as succession proceeded. These findings help improve our understanding of ANF activity in non-nodulating plants and N budgets in post glacial primary succession.

Revealing the transfer pathways of cyanobacterial-fixed N into the boreal forest through the feather-moss microbiome.

Introduction: Biological N2 fixation in feather-mosses is one of the largest inputs of new nitrogen (N) to boreal forest ecosystems; however, revealing the fate of newly fixed N within the bryosphere (i.e. bryophytes and their associated organisms) remains uncertain. Methods: Herein, we combined 15N tracers, high resolution secondary ion mass-spectrometry (NanoSIMS) and a molecular survey of bacterial, fungal and diazotrophic communities, to determine the origin and transfer pathways of newly fixed N2 within feather-moss (Pleurozium schreberi) and its associated microbiome. Results: NanoSIMS images reveal that newly fixed N2, derived from cyanobacteria, is incorporated into moss tissues and associated bacteria, fungi and micro-algae. Discussion: These images demonstrate that previous assumptions that newly fixed N2 is sequestered into moss tissue and only released by decomposition are not correct. We provide the first empirical evidence of new pathways for N2 fixed in feather-mosses to enter the boreal forest ecosystem (i.e. through its microbiome) and discuss the implications for wider ecosystem function.

Differentiating Sources of Fecal Contamination to Wilderness Waters Using Droplet Digital PCR and Fecal Indicator Bacteria Methods.

INTRODUCTION: Human activity in wilderness areas has the potential to affect aquatic ecosystems, including through the introduction of microorganisms associated with fecal contamination. We examined fecal microorganism contamination in water sources (lake outlets, snowmelt streams) in the popular Absaroka Beartooth Wilderness in the United States. Although the region is remote, increasing human visitation has the potential to negatively affect water quality, with particular concern about human-derived microorganism fecal contaminants. METHODS: We used standard fecal indicator bacterial assays that quantified total coliform bacteria and Escherichia coli concentrations, together with more specific polymerase chain reaction-based microbial assays that identified possible human sources of fecal microorganisms in these waters. RESULTS: Total coliforms were detected at all lake outlets (21 of 21 sites), and E coli was detected at 11 of 21 sites. Droplet digital polymerase chain reaction assays revealed the presence of human feces-derived microorganisms, albeit at abundances below the limit of detection (<10 gene copies per milliliter of water) at all but 1 of the sampling sites. CONCLUSIONS: Our results suggest low prevalence of water-borne pathogens (specifically E coli and human-derived Bacteroides) in this popular wilderness area. However, widespread detection of total coliforms, Bacteroides, and E coli highlight the importance of purifying water sources in wilderness areas before consumption. Specific sources of total coliforms and E coli in these waters remain unknown but could derive from wild or domesticated animals that inhabit or visit the Absaroka Beartooth Wilderness. Hence, although contamination by human fecal microorganisms appears minimal, human visitation could indirectly influence fecal contamination through domesticated animals.

Correction to: Long-Term Recovery of Microbial Communities in the Boreal Bryosphere Following Fire Disturbance.

The original version of this article contained an error in the Molecular Analysis subsection of the Methods.

Angiosperm symbioses with non-mycorrhizal fungal partners enhance N acquisition from ancient organic matter in a warming maritime Antarctic.

In contrast to the situation in plants inhabiting most of the world's ecosystems, mycorrhizal fungi are usually absent from roots of the only two native vascular plant species of maritime Antarctica, Deschampsia antarctica and Colobanthus quitensis. Instead, a range of ascomycete fungi, termed dark septate endophytes (DSEs), frequently colonise the roots of these plant species. We demonstrate that colonisation of Antarctic vascular plants by DSEs facilitates not only the acquisition of organic nitrogen as early protein breakdown products, but also as non-proteinaceous d-amino acids and their short peptides, accumulated in slowly-decomposing organic matter, such as moss peat. Our findings suggest that, in a warming maritime Antarctic, this symbiosis has a key role in accelerating the replacement of formerly dominant moss communities by vascular plants, and in increasing the rate at which ancient carbon stores laid down as moss peat over centuries or millennia are returned to the atmosphere as CO2 .

Quantifying the elemental composition of mosses in western Washington USA.

Major and trace element deposition across western Washington, USA was assessed in 2016 and 2017 by analyzing tissue metal concentrations in the epiphytic mosses Isothecium stoloniferum (Bridel) and Kindbergia praelonga (Hedw.) Ochyra. We used an intensive, vertically stratified sampling approach in Acer macrophyllum canopies in the Hoh Rainforest on the Olympic Peninsula, WA and in Seattle, WA to collect 214 samples of I. stoloniferum. An extensive, ground-based sampling approach was used across an urban-to-wildland gradient to collect 59 K. praelonga samples. Intensive samples were collected four times (April, July, and October of 2016 and in January 2017) and extensive samples three times (April, July, and October 2016) to assess seasonal differences in metal concentrations across sampling locations. A total of 273 moss samples were analyzed for Cd, Cr, Cu, Fe, K, Mg, Mn, Ni, Pb, Sr, Ti, and Zn concentrations. Elevated concentrations of these elements were found in moss samples from both intensive and extensive sampling efforts across all seasons. Sampling location for both intensive and extensive sampling efforts was found to be a significant factor in determining moss metal concentrations. Metal deposition in and around Seattle appears to be derived from the regional transportation sector and other industrial sources. Ten I. stoloniferum samples from Seattle and the Hoh Rainforest were analyzed for Pb and Sr isotope ratios to help differentiate between natural and industrial-based emission sources. Hoh Rainforest Pb isotopes appear to be explained by a mixture of long-range Asian Pb influences and natural Pb sources, whereas Seattle Pb isotopes appear driven by industrial and road dust sources.

Biochar additions alter phosphorus and nitrogen availability in agricultural ecosystems: A meta-analysis.

Biochar is a carbon (C) rich product of thermochemical conversion of organic material that is used as a soil amendment due to its resistance to decomposition and its influence on nutrient dynamics; however, individual studies on biochar effects on phosphorus (P) and nitrogen (N) have proven inconsistent. Herein, we performed a meta-analysis of 124 published studies to evaluate the influence of biochar on available P, microbial biomass P (MBP), and inorganic N (NO3--N and NH4+-N) in global agricultural ecosystems. Overall, the results showed that biochar applications significantly increased surface soil available P by 45% and MBP by 48% across the full range of biochar characteristics, soil type, or experimental conditions. By contrast, biochar addition to soil reduced NO3--N concentrations by 12% and NH4+-N by 11%, but in most cases biochar added in combination with organic fertilizer significantly increased soil NH4+-N compared to controls. Biochar C:N ratio and biochar source (feedstock) strongly influenced soil P availability response to biochar where inorganic N was most influenced by biochar C:N ratio and soil pH. Biochar made from manure or other low C:N ratio materials, generated at low temperatures, or applied at high rates were generally more effective at enhancing soil available P. It is important, however, to note that most negative results were observed in short-term (<6 months) where long-term studies (>12 months) tended to result in neutral to modest positive effects on both P and N. This meta-analysis indicates that biochar generally enhances soil P availability when added to soils alone or in combination with fertilizer. These findings provide a scientific basis for developing more rational strategies toward widespread adoption of biochar as a soil amendment for agricultural P and N management.

Anthropogenic deposition of heavy metals and phosphorus may reduce biological N2 fixation in boreal forest mosses.

A study was undertaken to test the effects of molybdenum (Mo) and phosphorus (P) amendments on biological nitrogen (N) fixation (BNF) by boreal forest moss-associated cyanobacteria. Feather moss (Pleurozium schreberi) samples were collected on five sites, on two dates and at different roadside distances (0-100m) corresponding to an assumed gradient of reactive N deposition. Potential BNF of Mo and P amended moss samples was measured using the acetylene reduction assay. Total N, P and heavy metal concentrations of mosses collected at 0 and 100m from roadsides were also measured. Likewise, the needles from Norway spruce trees (Picea abies) at different roadside distances were collected in late summer and analyzed for total N, P and heavy metals. There was a significant increase in BNF with roadside distance on 7-of-10 individual Site×Date combinations. We found no clear evidence of an N gradient across roadside distances. Elemental analyses of feather moss and Norway spruce needle tissues suggested decreasing deposition of heavy metals (Mo-Co-Cr-Ni-V-Pb-Ag-Cu) as well as P with increasing distance from the roadside. The effects of Mo and P amendments on BNF were infrequent and inconsistent across roadside distances and across sites. One particular site, however, displayed greater concentrations of heavy metals near the roadside, as well as a steeper P fertility gradient with roadside distance, than the other sites. Here, BNF increased with roadside distance only when moss samples were amended with P. Also at this site, BNF across all roadside distances was higher when mosses were amended with both Mo and P, suggesting a co-limitation of these two nutrients in controlling BNF. In summary, our study showed a potential for car emissions to increase heavy metals and P along roadsides and underscored the putative roles of these anthropogenic pollutants on BNF in northern latitudes.

Priorities for research in soil ecology.

The ecological interactions that occur in and with soil are of consequence in many ecosystems on the planet. These interactions provide numerous essential ecosystem services, and the sustainable management of soils has attracted increasing scientific and public attention. Although soil ecology emerged as an independent field of research many decades ago, and we have gained important insights into the functioning of soils, there still are fundamental aspects that need to be better understood to ensure that the ecosystem services that soils provide are not lost and that soils can be used in a sustainable way. In this perspectives paper, we highlight some of the major knowledge gaps that should be prioritized in soil ecological research. These research priorities were compiled based on an online survey of 32 editors of Pedobiologia - Journal of Soil Ecology. These editors work at universities and research centers in Europe, North America, Asia, and Australia.The questions were categorized into four themes: (1) soil biodiversity and biogeography, (2) interactions and the functioning of ecosystems, (3) global change and soil management, and (4) new directions. The respondents identified priorities that may be achievable in the near future, as well as several that are currently achievable but remain open. While some of the identified barriers to progress were technological in nature, many respondents cited a need for substantial leadership and goodwill among members of the soil ecology research community, including the need for multi-institutional partnerships, and had substantial concerns regarding the loss of taxonomic expertise.

Long-Term Recovery of Microbial Communities in the Boreal Bryosphere Following Fire Disturbance.

Our study used a ∼360-year fire chronosequence in northern Sweden to investigate post-fire microbial community dynamics in the boreal bryosphere (the living and dead parts of the feather moss layer on the forest floor, along with the associated biota). We anticipated systematic changes in microbial community structure and growth strategy with increasing time since fire (TSF) and used amplicon pyrosequencing to establish microbial community structure. We also recorded edaphic factors (relating to pH, C and N accumulation) and the physical characteristics of the feather moss layer. The molecular analyses revealed an unexpectedly diverse microbial community. The structure of the community could be largely explained by just two factors, TSF and pH, although the importance of TSF diminished as the forest recovered from disturbance. The microbial communities on the youngest site (TSF = 14 years) were clearly different from older locations (>100 years), suggesting relatively rapid post-fire recovery. A shift towards Proteobacterial taxa on older sites, coupled with a decline in the relative abundance of Acidobacteria, suggested an increase in resource availability with TSF. Saprotrophs dominated the fungal community. Mycorrhizal fungi appeared to decline in abundance with TSF, possibly due to changing N status. Our study provided evidence for the decadal-scale legacy of burning, with implications for boreal forests that are expected to experience more frequent burns over the course of the next century.

Variable Nitrogen Fixation in Wild Populus.

The microbiome of plants is diverse, and like that of animals, is important for overall health and nutrient acquisition. In legumes and actinorhizal plants, a portion of essential nitrogen (N) is obtained through symbiosis with nodule-inhabiting, N2-fixing microorganisms. However, a variety of non-nodulating plant species can also thrive in natural, low-N settings. Some of these species may rely on endophytes, microorganisms that live within plants, to fix N2 gas into usable forms. Here we report the first direct evidence of N2 fixation in the early successional wild tree, Populus trichocarpa, a non-leguminous tree, from its native riparian habitat. In order to measure N2 fixation, surface-sterilized cuttings of wild poplar were assayed using both 15N2 incorporation and the commonly used acetylene reduction assay. The 15N label was incorporated at high levels in a subset of cuttings, suggesting a high level of N-fixation. Similarly, acetylene was reduced to ethylene in some samples. The microbiota of the cuttings was highly variable, both in numbers of cultured bacteria and in genetic diversity. Our results indicated that associative N2-fixation occurred within wild poplar and that a non-uniformity in the distribution of endophytic bacteria may explain the variability in N-fixation activity. These results point to the need for molecular studies to decipher the required microbial consortia and conditions for effective endophytic N2-fixation in trees.

Intensive land use in the Swedish mountains between AD 800 and 1200 led to deforestation and ecosystem transformation with long-lasting effects.

Anthropogenic deforestation has shaped ecosystems worldwide. In subarctic ecosystems, primarily inhabited by native peoples, deforestation is generally considered to be mainly associated with the industrial period. Here we examined mechanisms underlying deforestation a thousand years ago in a high-mountain valley with settlement artifacts located in subarctic Scandinavia. Using the Heureka Forestry Decision Support System, we modeled pre-settlement conditions and effects of tree cutting on forest cover. To examine lack of regeneration and present nutrient status, we analyzed soil nitrogen. We found that tree cutting could have deforested the valley within some hundred years. Overexploitation left the soil depleted beyond the capacity of re-establishment of trees. We suggest that pre-historical deforestation has occurred also in subarctic ecosystems and that ecosystem boundaries were especially vulnerable to this process. This study improves our understanding of mechanisms behind human-induced ecosystem transformations and tree-line changes, and of the concept of wilderness in the Scandinavian mountain range.

Diazotrophy in alluvial meadows of subarctic river systems.

There is currently limited understanding of the contribution of biological N2 fixation (diazotrophy) to the N budget of large river systems. This natural source of N in boreal river systems may partially explain the sustained productivity of river floodplains in Northern Europe where winter fodder was harvested for centuries without fertilizer amendments. In much of the world, anthropogenic pollution and river regulation have nearly eliminated opportunities to study natural processes that shaped early nutrient dynamics of large river systems; however, pristine conditions in northern Fennoscandia allow for the retrospective evaluation of key biochemical processes of historical significance. We investigated biological N2 fixation (diazotrophy) as a potential source of nitrogen fertility at 71 independent floodplain sites along 10 rivers and conducted seasonal and intensive analyses at a subset of these sites. Biological N2 fixation occurred in all floodplains, averaged 24.5 kg N ha(-1) yr(-1) and was down regulated from over 60 kg N ha(-1) yr(-1) to 0 kg N ha(-1) yr(-1) by river N pollution. A diversity of N2-fixing cyanobacteria was found to colonize surface detritus in the floodplains. The data provide evidence for N2 fixation to be a fundamental source of new N that may have sustained fertility at alluvial sites along subarctic rivers. Such data may have implications for the interpretation of ancient agricultural development and the design of contemporary low-input agroecosystems.

Bacterial endophytes enhance competition by invasive plants.

PREMISE OF THE STUDY: Invasive plants can alter soil microbial communities and profoundly alter ecosystem processes. In the invasive grass Sorghum halepense, these disruptions are consequences of rhizome-associated bacterial endophytes. We describe the effects of N2-fixing bacterial strains from S. halepense (Rout and Chrzanowski, 2009) on plant growth and show that bacteria interact with the plant to alter soil nutrient cycles, enabling persistence of the invasive. • METHODS: We assessed fluxes in soil nutrients for ∼4 yr across a site invaded by S. halepense. We assayed the N2-fixing bacteria in vitro for phosphate solubilization, iron chelation, and production of the plant-growth hormone indole-3-acetic acid (IAA). We assessed the plant's ability to recruit bacterial partners from substrates and vertically transmit endophytes to seeds and used an antibiotic approach to inhibit bacterial activity in planta and assess microbial contributions to plant growth. • KEY RESULTS: We found persistent alterations to eight biogeochemical cycles (including nitrogen, phosphorus, and iron) in soils invaded by S. halepense. In this context, three bacterial isolates solubilized phosphate, and all produced iron siderophores and IAA in vitro. In growth chamber experiments, bacteria were transmitted vertically, and molecular analysis of bacterial community fingerprints from rhizomes indicated that endophytes are also horizontally recruited. Inhibiting bacterial activity with antibiotics resulted in significant declines in plant growth rate and biomass, with pronounced rhizome reductions. • CONCLUSIONS: This work suggests a major role of endophytes on growth and resource allocation of an invasive plant. Indeed, bacterial isolate physiology is correlated with invader effects on biogeochemical cycles of nitrogen, phosphate, and iron.

Moss-cyanobacteria associations as biogenic sources of nitrogen in boreal forest ecosystems.

The biological fixation of atmospheric nitrogen (N) is a major pathway for available N entering ecosystems. In N-limited boreal forests, a significant amount of N2 is fixed by cyanobacteria living in association with mosses, contributing up to 50% to the total N input. In this review, we synthesize reports on the drivers of N2 fixation in feather moss-cyanobacteria associations to gain a deeper understanding of their role for ecosystem-N-cycling. Nitrogen fixation in moss-cyanobacteria associations is inhibited by N inputs and therefore, significant fixation occurs only in low N-deposition areas. While it has been shown that artificial N additions in the laboratory as well as in the field inhibit N2 fixation in moss-cyanobacteria associations, the type, as well as the amounts of N that enters the system, affect N2 fixation differently. Another major driver of N2 fixation is the moisture status of the cyanobacteria-hosting moss, wherein moist conditions promote N2 fixation. Mosses experience large fluctuations in their hydrological status, undergoing significant natural drying and rewetting cycles over the course of only a few hours, especially in summer, which likely compromises the N input to the system via N2 fixation. Perhaps the most central question, however, that remains unanswered is the fate of the fixed N2 in mosses. The cyanobacteria are likely to leak N, but whether this N is transferred to the soil and if so, at which rates and timescales, is unknown. Despite our increasing understanding of the drivers of N2 fixation, the role moss-cyanobacteria associations play in ecosystem-N-cycling remains unresolved. Further, the relationship mosses and cyanobacteria share is unknown to date and warrants further investigation.

The cyanobacterial role in the resistance of feather mosses to decomposition--toward a new hypothesis.

Cyanobacteria-plant symbioses play an important role in many ecosystems due to the fixation of atmospheric nitrogen (N) by the cyanobacterial symbiont. The ubiquitous feather moss Pleurozium schreberi (Brid.) Mitt. is colonized by cyanobacteria in boreal systems with low N deposition. Here, cyanobacteria fix substantial amounts of N2 and represent a potential N source. The feather moss appears to be resistant to decomposition, which could be partly a result of toxins produced by cyanobacteria. To assess how cyanobacteria modulated the toxicity of moss, we measured inhibition of bacterial growth. Moss with varying numbers of cyanobacteria was added to soil bacteria to test the inhibition of their growth using the thymidine incorporation technique. Moss could universally inhibit bacterial growth, but moss toxicity did not increase with N2 fixation rates (numbers of cyanobacteria). Instead, we see evidence for a negative relationship between moss toxicity to bacteria and N2 fixation, which could be related to the ecological mechanisms that govern the cyanobacteria-moss relationship. We conclude that cyanobacteria associated with moss do not contribute to the resistance to decomposition of moss, and from our results emerges the question as to what type of relationship the moss and cyanobacteria share.

Acquisition and assimilation of nitrogen as peptide-bound and D-enantiomers of amino acids by wheat.

Nitrogen is a key regulator of primary productivity in many terrestrial ecosystems. Historically, only inorganic N (NH(4)(+) and NO(3)(-)) and L-amino acids have been considered to be important to the N nutrition of terrestrial plants. However, amino acids are also present in soil as small peptides and in D-enantiomeric form. We compared the uptake and assimilation of N as free amino acid and short homopeptide in both L- and D-enantiomeric forms. Sterile roots of wheat (Triticum aestivum L.) plants were exposed to solutions containing either (14)C-labelled L-alanine, D-alanine, L-trialanine or D-trialanine at a concentration likely to be found in soil solution (10 µM). Over 5 h, plants took up L-alanine, D-alanine and L-trialanine at rates of 0.9±0.3, 0.3±0.06 and 0.3±0.04 µmol g(-1) root DW h(-1), respectively. The rate of N uptake as L-trialanine was the same as that as L-alanine. Plants lost ca.60% of amino acid C taken up in respiration, regardless of the enantiomeric form, but more (ca.80%) of the L-trialanine C than amino acid C was respired. When supplied in solutions of mixed N form, N uptake as D-alanine was ca.5-fold faster than as NO(3)(-), but slower than as L-alanine, L-trialanine and NH(4)(+). Plants showed a limited capacity to take up D-trialanine (0.04±0.03 µmol g(-1) root DW h(-1)), but did not appear to be able to metabolise it. We conclude that wheat is able to utilise L-peptide and D-amino acid N at rates comparable to those of N forms of acknowledged importance, namely L-amino acids and inorganic N. This is true even when solutes are supplied at realistic soil concentrations and when other forms of N are available. We suggest that it may be necessary to reconsider which forms of soil N are important in the terrestrial N cycle.

Contribution of crenarchaeal autotrophic ammonia oxidizers to the dark primary production in Tyrrhenian deep waters (Central Mediterranean Sea).

Mesophilic Crenarchaeota have recently been thought to be significant contributors to nitrogen (N) and carbon (C) cycling. In this study, we examined the vertical distribution of ammonia-oxidizing Crenarchaeota at offshore site in Southern Tyrrhenian Sea. The median value of the crenachaeal cell to amoA gene ratio was close to one suggesting that virtually all deep-sea Crenarchaeota possess the capacity to oxidize ammonia. Crenarchaea-specific genes, nirK and ureC, for nitrite reductase and urease were identified and their affiliation demonstrated the presence of 'deep-sea' clades distinct from 'shallow' representatives. Measured deep-sea dark CO(2) fixation estimates were comparable to the median value of photosynthetic biomass production calculated for this area of Tyrrhenian Sea, pointing to the significance of this process in the C cycle of aphotic marine ecosystems. To elucidate the pivotal organisms in this process, we targeted known marine crenarchaeal autotrophy-related genes, coding for acetyl-CoA carboxylase (accA) and 4-hydroxybutyryl-CoA dehydratase (4-hbd). As in case of nirK and ureC, these genes are grouped with deep-sea sequences being distantly related to those retrieved from the epipelagic zone. To pair the molecular data with specific functional attributes we performed [(14)C]HCO(3) incorporation experiments followed by analyses of radiolabeled proteins using shotgun proteomics approach. More than 100 oligopeptides were attributed to 40 marine crenarchaeal-specific proteins that are involved in 10 different metabolic processes, including autotrophy. Obtained results provided a clear proof of chemolithoautotrophic physiology of bathypelagic crenarchaeota and indicated that this numerically predominant group of microorganisms facilitate a hitherto unrecognized sink for inorganic C of a global importance.

Interactive effects of historical logging and fire exclusion on ponderosa pine forest structure in the northern Rockies.

Increased forest density resulting from decades of fire exclusion is often perceived as the leading cause of historically aberrant, severe, contemporary wildfires and insect outbreaks documented in some fire-prone forests of the western United States. Based on this notion, current U.S. forest policy directs managers to reduce stand density and restore historical conditions in fire-excluded forests to help minimize high-severity disturbances. Historical logging, however, has also caused widespread change in forest vegetation conditions, but its long-term effects on vegetation structure and composition have never been adequately quantified. We document that fire-excluded ponderosa pine forests of the northern Rocky Mountains logged prior to 1960 have much higher average stand density, greater homogeneity of stand structure, more standing dead trees and increased abundance of fire-intolerant trees than paired fire-excluded, unlogged counterparts. Notably, the magnitude of the interactive effect of fire exclusion and historical logging substantially exceeds the effects of fire exclusion alone. These differences suggest that historically logged sites are more prone to severe wildfires and insect outbreaks than unlogged, fire-excluded forests and should be considered a high priority for fuels reduction treatments. Furthermore, we propose that ponderosa pine forests with these distinct management histories likely require distinct restoration approaches. We also highlight potential long-term risks of mechanical stand manipulation in unlogged forests and emphasize the need for a long-term view of fuels management.