Transformation of soil organic matter in microarthropod community from the northern taiga of west Siberia

Recolonization of defaunated soil by springtails as well as by gamasid and oribatid mites and the changes in organic matter content of soil were studied in the northern taiga. After a one-year exposure in gauze bags (1.7 mm mesh), the abundance of microarthropods was higher but the number of species was lower compared to the surrounding soil. Large surface and litter forms did not colonize the samples, while the number of small and/or soil forms was higher. Soil samples inaccessible for microarthropods (0.15 mm mesh) were depleted of organic carbon compared to both surrounding soil and recolonized samples. The content of humic and fulvic acids was higher in the samples inaccessible to microarthropods. Humification processes prevailed in soils in the absence of microarthropods.     

The fleas of small mammals in the northern taiga of western Siberia

Data on the species composition of fleas, their abundance and distribution on hosts and on territory are given. Changes in the species composition and abundance of fleas in the latitude and meridional directions are shown.     

Glycosylation of purified buffalo heart galectin-1 plays crucial role in maintaining its structural and functional integrity

A buffalo heart galectin-1 purified by gel filtration chromatography revealed the presence of 3.55% carbohydrate content, thus it is the first mammalian heart galectin found to be glycosylated in nature and emphasizes the need to perform deglycosylation studies. Physicochemical comparative analysis between the properties of the native and deglycosylated proteins was carried out to understand the significance of glycosylation. The deglycosylated protein exhibited lesser thermal and pH stability compared to the native galectin. When exposed to thiol blocking reagents, denaturants, and detergents, remarkable differences were observed in the properties of the native and deglycosylated protein. Compared to the native glycosylated protein, the deglycosylated galectin showed enhanced fluorescence quenching when exposed to various agents. CD and FTIR analysis showed that deglycosylation of the purified galectin and its exposure to different chemicals resulted in significant deviations from regular secondary structure of the protein, thus emphasizing the significance of glycosylation for maintaining the active conformation of the protein. The remarkable differences observed in the properties of the native and deglycosylated galectin add an important dimension to the significance of protein glycosylation and its associated biological and clinical relevance.     

Soil arthropoda of post-fire successions in northern taiga of West Siberia

The soil arthropoda population of northern taiga was investigated in the primary pine forest which had not been subject to any fire for at least 100 years and at two burnt sites of different opost-fire successions. The population of the primary nonburnt forest is represented by 54 microarthropoda species. The mesofauna is composed almost exceptionally of spiders: 10 species of them were identified. The foliage underwood develops on young burnt sites; the soil is covered with thick mossy cushions, with spots of reedgrass. The density of collembolan and oribatid mite population there is about two times lower than in nonburnt pine forests; gamasid mites are absent. The microarthropoda population is represented by the species which are common in the surrounding primary pine forests. The mesofauna consists mainly of ground beetles, open-land predators, and myxophytophagans. Spiders are represented by some widespread mobile species of low density. A mixed forest with mossy-lichen cover is formed on old burnt sites (of an age of about 50 years). Diversity and density of microarthropoda increase reaching the values characteristic of the primary forest; however, the species composition and dominance are still different. The fraction of spiders in mesofauna increases. The ground beetle population is the most abundant and diverse.     

Structure of plant communities in the early succession stages on anthropogenic sandy outcrops of the forest tundra and northern taiga of Western Siberia

The results of a study of the taxonomic, ecological, and phytocenotic structure of plant communities formed in the early stages of overgrowth of the anthropogenic sandy outcrops within the forest-tundra zone and northern taiga forest subzone of Western Siberia are presented. In the early stages of vegetativecover restoration, there are from 2 to 11 species growing into sparse communities of the classes Loiseleurio-Vaccinietea, Artemisietea vulgaris, and Koelerio-Corynephoretea. The participation of some meso-xerophytic forest-tundra, meadow-margin, and weed herbaceous plant and dwarf shrubs species, mostly with ruderal and stress-tolerant eco-phytocenotic strategies, as well as with secondary strategies—violent-ruderal and ruderal–stress-tolerant—in the secondary succession on the sandy outcrops have been shown. The primary succession begins at the bottom and slopes of the pit ditches, as well on the surface of the sand dunes, and proceeds at an accelerated scenario. Hygro-, meso- and xerophilous species, predominantly oligo-mesotrophic rhizome and densely firm-bunch grasses and shrubs of the native flora, as well as ground lichens, participate in the early stages of succession.     

Dual role of Zn in maintaining structural integrity and suppressing deacetylase activity of SIRT1

Zn²⁺ directly participates in catalysis of histone deacetylase (HDAC) Classes I, II, IV enzymes while its role in HDAC Class III activity is not well established. Herein we investigated the effects of Zn²⁺ on the deacetylase activity of sirtuin 1 (silent mating type information regulation 2 homolog 1, SIRT1). We found that the inherent Zn²⁺ at the zinc-finger motif of SIRT1 is essential for the structural integrity and the deacetylase activity of SIRT1, whereas the exogenous Zn²⁺ strongly inhibits the deacetylase activity with an IC₅₀ of 0.82 μM for Zn(Gly)₂. SIRT1 activity suppressed by the exogenous Zn²⁺ can be fully recovered by the metal chelator EDTA but not by the activator resveratrol. We also identified Zn²⁺ as a noncompetitive inhibitor for the substrates of NAD⁺ and the acetyl peptide P53-AMC. The 8-anilino-1-naphthalenesulfonic acid (ANS) fluorescence titration experiments and site-directed mutagenesis study suggested that the exogenous Zn²⁺ binds to SIRT1 but not at the zinc-finger motif. These results indicate that Zn²⁺ plays a dual role in SIRT1 activity. Inherent Zn²⁺ at the zinc-finger motif is structurally related and essential for SIRT1 activity. On the other hand, Zn²⁺ may also bind to another site different from the zinc-finger motif or the binding sites for the substrates or resveratrol and act as a potent inhibitor of SIRT1.     

Climatically induced interannual variability in aboveground production in forest-tundra and northern taiga of central Siberia

To investigate the variability of primary production of boreal forest ecosystems under the current climatic changes, we compared the dynamics of annual increments and productivity of the main components of plant community (trees, shrubs, mosses) at three sites in the north of Siberia (Russia). Annual radial growth of trees and shrubs was mostly defined by summer temperature regime (positive correlation), but climatic response of woody plants was species specific and depends on local conditions. Dynamics of annual increments of mosses were opposite to tree growth. The difference in climatic response of the different vegetation components of the forest ecosystems indicates that these components seem to be adapted to use climatic conditions during the short and severe northern summer, and decreasing in annual production of one component is usually combined with the increase of other component productivity. Average productivity in the northern forest ecosystems varies from 0.05 to 0.14 t ha⁻¹ year⁻¹ for trees, from 0.05 to 0.18 t ha⁻¹ year⁻¹ for shrubs and from 0.54 to 0.66 t ha⁻¹ year⁻¹ for mosses. Higher values of tree productivity combined with lower annual moss productivity were found in sites in northern taiga in comparison with forest-tundra. Different tendencies in the productivity of the dominant species from each vegetation level (trees, shrubs, mosses) were indicated for the last 10 years studied (1990–1999): while productivity of mosses is increasing, productivity of trees is decreasing, but there is no obvious trend in the productivity of shrubs. Our results show that in the long term, the main contribution to changes in annual biomass productivity in forest-tundra and northern taiga ecosystems under the predicted climatic changes will be determined by living ground cover.     

The role of carrion in maintaining biodiversity and ecological processes in terrestrial ecosystems

Carrion provides a resource for a subset of animal species that deliver a critical ecosystem service by consuming dead animal matter and recycling its nutrients. A growing number of studies have also shown various effects of carrion on different plant and microbial communities. However, there has been no review of these studies to bring this information together and identify priority areas for future research. We review carrion ecology studies from the last two decades and summarise the range of spatial and temporal effects of carrion on soil nutrients, microbes, plants, arthropods, and vertebrates. We identify key knowledge gaps in carrion ecology, and discuss how closing these gaps can be achieved by focusing future research on the (1) different kinds of carrion resources, (2) interactions between different components of the carrion community, (3) the ways that ecosystem context can moderate carrion effects, and (4) considerations for carrion management. To guide this research, we outline a framework that builds on the ‘ephemeral resource patch’ concept, and helps to structure research questions that link localised effects of carrion with their consequences at landscape scales. This will enable improved characterisation of carrion as a unique resource pool, provide answers for land managers in a position to influence carrion availability, and establish the ways that carrion affects the dynamics of species diversity and ecological processes within landscapes.     

Contribution of winter processes to soil nitrogen flux in taiga forest ecosystems

We measured annual net nitrogen (N) mineralization, nitrification, and amino acid production in situ across a primary successional sequence in interior Alaska, USA. Net N mineralization per gram dry soil increased across the successional sequence, but with a sharp decline in the oldest stage (black spruce). Net N mineralization expressed per gram soil organic matter exhibited the opposite pattern, suggesting that soil organic matter quality decreases significantly across succession. Net N mineralization rates during the growing season from green-up (early May) through freeze-up (late September–early October) accounted for approximately 60% of the annual inorganic N flux, whereas the remaining N was released during the apparent dormant season. Nitrogen release during winter occurred primarily during October–January with only negligible N mineralization during early spring in stands of willow, alder, balsam poplar and white spruce. By contrast, black spruce stands exhibited substantial mineralization after snow melt during early spring. The high rates of N mineralization in late autumn through early winter coincide with high turnover of fine root biomass in these stands, suggesting that labile substrate production, rather than temperature, is a major controlling factor over N release in these ecosystems. We suggest that the convention of restricting measurements of soil processes to the growing season greatly underestimate annual flux rates of inorganic nitrogen in these high-latitude ecosystems.     

The functional role of producer diversity in ecosystems

Over the past several decades, a rapidly expanding field of research known as biodiversity and ecosystem functioning has begun to quantify how the world's biological diversity can, as an independent variable, control ecological processes that are both essential for, and fundamental to, the functioning of ecosystems. Research in this area has often been justified on grounds that (1) loss of biological diversity ranks among the most pronounced changes to the global environment and that (2) reductions in diversity, and corresponding changes in species composition, could alter important services that ecosystems provide to humanity (e.g., food production, pest/disease control, water purification). Here we review over two decades of experiments that have examined how species richness of primary producers influences the suite of ecological processes that are controlled by plants and algae in terrestrial, marine, and freshwater ecosystems. Using formal meta-analyses, we assess the balance of evidence for eight fundamental questions and corresponding hypotheses about the functional role of producer diversity in ecosystems. These include questions about how primary producer diversity influences the efficiency of resource use and biomass production in ecosystems, how primary producer diversity influences the transfer and recycling of biomass to other trophic groups in a food web, and the number of species and spatial /temporal scales at which diversity effects are most apparent. After summarizing the balance of evidence and stating our own confidence in the conclusions, we outline several new questions that must now be addressed if this field is going to evolve into a predictive science that can help conserve and manage ecological processes in ecosystems.     

Antioxidant role of autophagy in maintaining the integrity of glomerular capillaries

Autophagy is a lysosomal degradation system by which cytosolic materials and damaged organelles are broken down into basic components. To explore the physiological role of autophagy in glomerular endothelial cells (GEnCs), we compared the autophagic flux among cells in the kidney under starvation. Inhibition of autophagy by chloroquine administration significantly increased the number of autophagosomes or autolysosomes in GEnCs and proximal tubular cells, but not in podocytes, suggesting that the GEnCs exhibit substantial autophagic activity. Next, we analyzed endothelial and hematopoietic cell-specific atg5-deficient mice (atg5-conditional KO [cKO] mice). Glomeruli of 4-wk-old atg5-cKO mice exhibited slightly distended capillary loops accompanied by an accumulation of reactive oxygen species (ROS). Glomeruli of 8-wk-old atg5-cKO mice showed a lobular pattern with thickening of the capillary loops and mesangial matrix expansion; however, the vasculature of other organs was preserved. The atg5-cKO mice died by 12 wk of age, presumably due to pancytopenia resulting from the defect in their hematopoietic lineages. Therefore, we subjected 4-wk atg5-cKO mice to irradiation followed by bone marrow transplantation from normal littermates. Transplanted mice recapitulated the glomerular phenotypes of the atg5-cKO mice with no obvious histological changes in other organs. Twelve-mo-old transplanted mice developed mesangiolysis and glomerulosclerosis with significant deterioration of kidney function. Administration of N-acetyl-l-cysteine, a ROS scavenger, to atg5-cKO mice rescued the glomerular phenotypes. These data suggest that endothelial autophagy protects glomeruli from oxidative stress and maintains the integrity of glomerular capillaries. Enhancing endothelial autophagy may provide a novel therapeutic approach to minimizing glomerular diseases.     

The functional role of burrowing bivalves in freshwater ecosystems

1. Freshwater systems are losing biodiversity at a rapid rate, yet we know little about the functional role of most of this biodiversity. The ecosystem roles of freshwater burrowing bivalves have been particularly understudied. Here we summarize what is known about the functional role of burrowing bivalves in the orders Unionoida and Veneroida in lakes and streams globally. 2. Bivalves filter phytoplankton, bacteria and particulate organic matter from the water column. Corbicula and sphaeriids also remove organic matter from the sediment by deposit feeding, as may some unionids. Filtration rate varies with bivalve species and size, temperature, particle size and concentration, and flow regime. 3. Bivalves affect nutrient dynamics in freshwater systems, through excretion as well as biodeposition of faeces and pseudofaeces. Excretion rates are both size and species dependent, are influenced by reproductive stage, and vary greatly with temperature and food availability. 4. Bioturbation of sediments through bivalve movements increases sediment water and oxygen content and releases nutrients from the sediment to the water column. The physical presence of bivalve shells creates habitat for epiphytic and epizoic organisms, and stabilizes sediment and provides refugia for benthic fauna. Biodeposition of faeces and pseudofaeces can alter the composition of benthic communities. 5. There is conflicting evidence concerning the role of resource limitation in structuring bivalve communities. Control by bivalves of primary production is most likely when their biomass is large relative to the water volume and where hydrologic residence time is long. Future studies should consider exactly what bivalves feed upon, whether feeding varies seasonally and with habitat, and whether significant overlap in diet occurs. In particular, we need a clearer picture of the importance of suspension versus deposit feeding and the potential advantages and tradeoffs between these two feeding modes. 6. In North America, native burrowing bivalves (Unionidae) are declining at a catastrophic rate. This significant loss of benthic biomass, coupled with the invasion of an exotic burrowing bivalve (Corbicula), may result in large alterations of ecosystem processes and functions.     

The Caenorhabditis elegans aristaless orthologue, alr-1, is required for maintaining the functional and structural integrity of the amphid sensory organs

The homeobox-containing aristaless-related protein ARX has been directly linked to the development of a number of human disorders involving mental retardation and epilepsy and clearly plays a critical role in development of the vertebrate central nervous system. In this work, we investigate the role of ALR-1, the Caenorhabditis elegans aristaless orthologue, in amphid sensory function. Our studies indicate that ALR-1 is required for maintenance of the amphid organ structure throughout larval development. Mutant analysis indicates a progressive loss in the amphid neurons' ability to fill with lipophilic dyes as well as a declining chemotactic response. The degeneration in amphid function corresponds with a failure of the glial-like amphid socket cell to maintain its specific cell shape and cell-cell contacts. Consistent with ALR-1 expression within the amphid socket cell, our results indicate a cell autonomous role for ALR-1 in maintaining cell shape. Furthermore, we demonstrate a role for ALR-1 in the proper morphogenesis of the anterior hypodermis. Genetic interaction tests also suggest that ALR-1 may function cooperatively with the cell adhesion processes in maintaining the amphid sensory organs.     

Dual role for Zn2+ in maintaining structural integrity and inducing DNA sequence specificity in a promiscuous endonuclease

We describe two uncommon roles for Zn2+ in enzyme KpnI restriction endonuclease (REase). Among all of the REases studied, KpnI REase is unique in its DNA binding and cleavage characteristics. The enzyme is a poor discriminator of DNA sequences, cleaving DNA in a promiscuous manner in the presence of Mg2+. Unlike most Type II REases, the active site of the enzyme comprises an HNH motif, which can accommodate Mg2+, Mn2+, or Ca2+. Among these metal ions, Mg2+ and Mn2+ induce promiscuous cleavage by the enzyme, whereas Ca2+-bound enzyme exhibits site-specific cleavage. Examination of the sequence of the protein revealed the presence of a zinc finger CCCH motif rarely found in proteins of prokaryotic origin. The zinc binding motif tightly coordinates zinc to provide a rigid structural framework for the enzyme needed for its function. In addition to this structural scaffold, another atom of zinc binds to the active site to induce high fidelity cleavage and suppress the Mg2+- and Mn2+-mediated promiscuous behavior of the enzyme. This is the first demonstration of distinct structural and catalytic roles for zinc in an enzyme, suggesting the distinct origin of KpnI REase.     

Assessing the functional implications of soil biodiversity in ecosystems

Soil communities are among the most species-rich components of terrestrial ecosystems. A major challenge for soil ecologists is to formulate feasible research strategies that will preserve and capitalize on the biodiversity resources of the soil. This article considers the role of soil organism diversity by concentrating on: (i) the relationship between soil biodiversity and ecosystem function; (ii) what issues need to be explored; (iii) studies carried out in the Ecotron controlled environment facility; and (iv) how stable isotope techniques can improve our understanding of the relationship between soil biodiversity and ecosystem function. It is advocated that: (i) the objective of any soil biodiversity study should always be the generation of general concepts, rather than local, system-specific observations; and (ii) any empirical study can be properly interpreted only within a quantitative ecological framework.     

The carbon balance in natural and disturbed forests of the southern taiga in central Siberia

Abstract. We evaluated the balance of production and decomposition in natural ecosystems of Pinus sylvestris, Larix sibirica and Betula pendula in the southern boreal forests of central Siberia, using the Yenisei transect. We also investigated whether anthropogenic disturbances (logging, fire and recreation pressure) influence the carbon budget. Pinus and Larix stands up to age class VI act as a net sink for atmospheric carbon. Mineralization rates in young Betula forests exceed rates of uptake via photosynthesis assimilation. Old‐growth stands of all three forest types are CO₂ sources to the atmosphere. The prevalence of old‐growth Larix in the southern taiga suggests that Larix stands are a net source of CO₂. The CO₂ flux to the atmosphere exceeds the uptake of atmospheric carbon via photosynthesis by 0.23 t C.ha^‐1.yr^‐1 (47%). Betula and Pinus forests are net sinks, as photosynthesis exceeds respiration by 13% and 16% respectively. The total carbon flux from Pinus, Larix and Betula ecosystems to the atmosphere is 10 387 thousand tons C.yr^‐1. Net Primary Production (0.935 t‐C.ha^‐1) exceeds carbon release from decomposition of labile and mobile soil organic matter (Rh) by 767 thousand tons C (0.064 t‐C.ha^‐1), so that these forests are net C‐sinks. The emissions due to decomposition of slash (101 thousand tons C; 1.0%) and from fires (0.21%) are very small. The carbon balance of human‐disturbed forests is significantly different. A sharp decrease in biomass stored in Pinus and Betula ecosystems leads to decreased production. As a result, the labile organic matter pool decreased by 6–8 times; course plant residues with a low decomposition rate thus dominate this pool. Annual carbon emissions to the atmosphere from these ecosystems are determined primarily by decomposing fresh litterfall. This source comprises 40–79% of the emissions from disturbed forests compared to only 13–28% in undisturbed forests. The ratio of emissions to production (NPP) is 20–30% in disturbed and 52–76% in undisturbed forests.     

Above- and below-ground phytomass and net primary production in boreal mire ecosystems of Western Siberia

We measured phytomass stock and production in Western Siberian mire ecosystems (palsa, ridge, oligotrophic and mesotrophic hollows, fen). To determine the contribution of different phytomass fractions into total production, we developed a method to estimate below-ground production (BNP). Standing crop of living above-ground phytomass on treeless plots varied from 300 to 660 g m⁻², reaching maximum on palsa, where 81% of phytomass consisted of Sphagnum mosses and lichens. In the hollows and the fen, Sphagnum percentage varied from 70 to 95%. Standing crop of living below-ground phytomass varied from 325 to 1,210 g m⁻². It consisted of woody stems, stem bases, rhizomes and roots, with the latter contributing from 30 to 60%. Total production of mire ecosystems in northern taiga of Western Siberia ranged from 350 to 960 g m⁻² year⁻¹ and depended on microtopography of the ecosystem (the presence of permafrost and water table depth). Production of treeless plant communities located on the elevated sites depended on the presence of permafrost: in comparison with the ridge, palsa production was lower. Production on the low sites increased with increase pH and reached maximum (960 g m⁻² year⁻¹) in poor fens. Bryophytes were the major producers above ground. Their production varied from 100 to 272 g m⁻² year⁻¹ and reached maximum on ridges. BNP contributed 37–66%, increasing due to increased contribution of sedges.     

The resilience and functional role of moss in boreal and arctic ecosystems

CONTENTS: Summary 49 I. Mosses in the northern, high-latitude region 50 II. The role of moss in ecological resilience 51 III. Response of moss to disturbance 54 IV. Future research needs 60 V. Conclusions 62 Acknowledgements 62 References 62 SUMMARY: Mosses in northern ecosystems are ubiquitous components of plant communities, and strongly influence nutrient, carbon and water cycling. We use literature review, synthesis and model simulations to explore the role of mosses in ecological stability and resilience. Moss community responses to disturbance showed all possible responses (increases, decreases, no change) within most disturbance categories. Simulations from two process-based models suggest that northern ecosystems would need to experience extreme perturbation before mosses were eliminated. But simulations with two other models suggest that loss of moss will reduce soil carbon accumulation primarily by influencing decomposition rates and soil nitrogen availability. It seems clear that mosses need to be incorporated into models as one or more plant functional types, but more empirical work is needed to determine how to best aggregate species. We highlight several issues that have not been adequately explored in moss communities, such as functional redundancy and singularity, relationships between response and effect traits, and parameter vs conceptual uncertainty in models. Mosses play an important role in several ecosystem processes that play out over centuries - permafrost formation and thaw, peat accumulation, development of microtopography - and there is a need for studies that increase our understanding of slow, long-term dynamical processes.     

A role for myelin-associated peroxisomes in maintaining paranodal loops and axonal integrity

Demyelinating diseases of the nervous system cause axon loss but the underlying mechanisms are not well understood. Here we show by confocal and electron microscopy that in myelin-forming glia peroxisomes are associated with myelin membranes. When peroxisome biogenesis is experimentally perturbed in Pex5 conditional mouse mutants, myelination by Schwann cells appears initially normal. However, in nerves of older mice paranodal loops become physically unstable and develop swellings filled with vesicles and electron-dense material. This novel model of a demyelinating neuropathy demonstrates that peroxisomes serve an important function in the peripheral myelin compartment, required for long-term axonal integrity.