Where old meets new: An ecosystem study of methanogenesis in a reflooded agricultural peatland

Reflooding formerly drained peatlands has been proposed as a means to reduce losses of organic matter and sequester soil carbon for climate change mitigation, but a renewal of high methane emissions has been reported for these ecosystems, offsetting mitigation potential. Our ability to interpret observed methane fluxes in reflooded peatlands and make predictions about future flux trends is limited due to a lack of detailed studies of methanogenic processes. In this study we investigate methanogenesis in a reflooded agricultural peatland in the Sacramento Delta, California. We use the stable‐and radio‐carbon isotopic signatures of wetland sediment methane, ecosystem‐scale eddy covariance flux observations, and laboratory incubation experiments, to identify which carbon sources and methanogenic production pathways fuel methanogenesis and how these processes are affected by vegetation and seasonality. We found that the old peat contribution to annual methane emissions was large (~30%) compared to intact wetlands, indicating a biogeochemical legacy of drainage. However, fresh carbon and the acetoclastic pathway still accounted for the majority of methanogenesis throughout the year. Although temperature sensitivities for bulk peat methanogenesis were similar between open‐water (Q₁₀ = 2.1) and vegetated (Q₁₀ = 2.3) soils, methane production from both fresh and old carbon sources showed pronounced seasonality in vegetated zones. We conclude that high methane emissions in restored wetlands constitute a biogeochemical trade‐off with contemporary carbon uptake, given that methane efflux is fueled primarily by fresh carbon inputs.     

The role of cladocerans in tracking long-term change in shallow lake trophic status

Shallow lakes have been affected by a variety of human activities profoundly altering their ecological structure and function. Cladocerans have been used to track change resulting from a variety of drivers at a number of time scales. Aquatic macrophytes are well recognised as reflecting the ecological condition of a lake. Here, we compare the plant macrofossils with the sub-fossil cladoceran assemblages from 20 dated sediment cores. Co-correspondence analysis was used to determine the degree of commonality of change in community composition of the two biological groups through time. This analysis revealed very high levels of agreement in the nature and timing of change at all the sites examined with very high correlation coefficients between the axis 1 scores for macrofossils and cladocerans. Furthermore, at all sites a high proportion of the variance (min 20%, max 54%) in the macrofossil data was explained by the change in the cladoceran assemblage. Sub-fossil macrofossil and cladoceran assemblages, from at least from 1700 AD onwards, were examined in more detail at three sites: Ormesby Great Broad, Felbrigg Lake and Lake Søbygaard. There was very good accord in the main shifts of the cladoceran and macrofossil assemblages at all three sites. This may reflect the long-term shift in the principal focus of primary production from the benthic to the pelagic habitat. We suggest that the combination of their central position in the food-web and the presence of both pelagic and benthic taxa make cladocerans a strong candidate as the single best indicator of (palaeo) ecological condition related to changing trophic status and alteration in food-web structure in shallow lakes.     

Impacts of silviculture on genetic diversity in the native forest species Eucalyptus sieberi

Potential impacts of regeneration practices ongenetic diversity in the Australian nativeforest species Eucalyptus sieberi L.A.S.Johnson. (silvertop ash) were assessed usingDNA markers. Three different silviculturaltreatments were examined: clear-felling withaerial re-sowing, and the seed tree system withsite preparation by either burning ormechanical disturbance. In addition, twounharvested stands were chosen as controls. Atotal sample of 825 trees were genotyped at 35Mendelian markers: 26 single-copy nuclear RFLPsand 9 microsatellites. No significantdifferences were found among the treatments inany of four population genetic statistics:allelic richness, effective number of alleles,expected heterozygosity and the panmictic index(f). Rare alleles were prevalent, and a MonteCarlo simulation showed that the apparent lossof four rare alleles from the saplingregenerants was highly statisticallysignificant. There was no evidence for recentbottlenecks from analyses of either the levelsof expected heterozygosity relative to thatexpected under mutation drift equilibrium, orthe allele frequency profiles. A dendrogram ofthe relationships between the sampledpopulations suggested that the seed tree systemmay result in the promotion of genetic drift(slight expansion of the dendrogram) whileaerial re-sowing of clear falls with the sameseedlot will lead to genetic homogenisation(contraction of the dendrogram). The apparentgenetic robustness of E. sieberi tonative forest regeneration practices isattributed to its local abundance combined withthe favourable properties of its reproductivebiology, as well as to the limitation that onlya single rotation was examined.     

Meta-analysis in applied ecology

This overview examines research synthesis in applied ecology and conservation. Vote counting and pooling unweighted averages are widespread despite the superiority of syntheses based on weighted combination of effects. Such analyses allow exploration of methodological uncertainty in addition to consistency of effects across species, space and time, but exploring heterogeneity remains controversial. Meta-analyses are required to generalize in ecology, and to inform evidence-based decision-making, but the more sophisticated statistical techniques and registers of research used in other disciplines must be employed in ecology to fully realize their benefits.     

Bacterial lipoprotein induces resistance to Gram-negative sepsis in TLR4-deficient mice via enhanced bacterial clearance

TLRs are highly conserved pathogen recognition receptors. As a result, TLR4-deficient C3H/HeJ mice are highly susceptible to Gram-negative sepsis. We have previously demonstrated that tolerance induced by bacterial lipoprotein (BLP) protects wild-type mice against polymicrobial sepsis-induced lethality. In this study, we assessed whether pretreatment of C3H/HeJ mice with BLP could induce resistance to a subsequent Gram-negative Salmonella typhimurium infection. Pretreatment with BLP resulted in a significant survival benefit in TLR4-deficient C3H/HeJ mice (p < 0.0002 vs control C3H/HeJ) after challenge with live S. typhimurium (0.25 x 10(6) CFU/mouse). This survival benefit was associated with enhanced bacterial clearance from the circulation and in the visceral organs (p < 0.05 vs control C3H/HeJ). Furthermore, pretreatment with BLP resulted in significant increases in complement receptor type 3 (CR3) and FcgammaIII/IIR expression on polymorphonuclear neutrophils (PMNs) and macrophages (p < 0.05 vs control C3H/HeJ). There was impaired bacterial recognition and phagocytosis in TLR4-deficient mice compared with wild-type mice. However, a significant augmented uptake, ingestion, and intracellular killing of S. typhimurium by PMNs and peritoneal macrophages was evident in BLP-pretreated C3H/HeJ mice (p < 0.05 vs control C3H/HeJ). An up-regulation of inducible NO synthase and increased production of intracellular NO were observed in peritoneal macrophages from BLP-pretreated C3H/HeJ mice (p < 0.05 vs control C3H/HeJ). Depletion of PMNs did not diminish the beneficial effects of BLP with regard to both animal survival and bacterial clearance. These results indicate that BLP, a TLR2 ligand, protects highly susceptible TLR4-deficient mice from Gram-negative sepsis via enhanced bacterial clearance.     

Insights into the molecular determinants of substrate specificity in glycoside hydrolase family 5 revealed by the crystal structure and kinetics of Cellvibrio mixtus mannosidase 5A

The enzymatic hydrolysis of the glycosidic bond is central to numerous biological processes. Glycoside hydrolases, which catalyze these reactions, are grouped into families based on primary sequence similarities. One of the largest glycoside hydrolase families is glycoside hydrolase family 5 (GH5), which contains primarily endo-acting enzymes that hydrolyze beta-mannans and beta-glucans. Here we report the cloning, characterization, and three-dimensional structure of the Cellvibrio mixtus GH5 beta-mannosidase (CmMan5A). This enzyme releases mannose from the nonreducing end of mannooligosaccharides and polysaccharides, an activity not previously observed in this enzyme family. CmMan5A contains a single glycone (-1) and two aglycone (+1 and +2) sugar-binding subsites. The -1 subsite displays absolute specificity for mannose, whereas the +1 subsite does not accommodate galactosyl side chains but will bind weakly to glucose. The +2 subsite is able to bind to decorated mannose residues. CmMan5A displays similar activity against crystalline and amorphous mannans, a property rarely attributed to glycoside hydrolases. The 1.5 A crystal structure reveals that CmMan5A adopts a (beta/alpha)(8) barrel fold, and superimposition with GH5 endo-mannanases shows that dramatic differences in the length of three loops modify the active center accessibility and thus modulate the specificity from endo to exo. The most striking and significant difference is the extended loop between strand beta8 and helix alpha8 comprising residues 378-412. This insertion forms a "double" steric barrier, formed by two short beta-strands that function to "block" the substrate binding cleft at the edge of the -1 subsite forming the "exo" active center topology of CmMan5A.     

Total cellular activity and distribution of a subpopulation of galactosyl receptors in isolated rat hepatocytes are differentially affected by microtubule drugs,monensin, low temperature,and chloroquine

We studied the effects of low temperature (20–37°C), monensin, chloroquine, and microtubule drugs on the cellular distribution and activity of galactosyl (Gal) receptors in isolated rat hepatocytes. After equilibration at 37°C, hepatocytes were incubated at 37°C, 31°C, 25°C, or 20°C or treated with or without inhibitors at 37°C in the absence of ligand. The cells were then assayed at 4°C for ¹²⁵I-asialo-orosomucoid binding, to measure receptor activity, or ¹²⁵I-anti-Gal receptor IgG binding, to measure receptor protein. Surface or total (surface and intracellular) Gal receptor activity and protein were measured on intact or digitonin-permeabilized cells, respectively. These inhibitors fell into two categories. Type I inhibitors (sub-37°C temperatures or colchicine) induced receptor redistribution but not inactivation. Treated cells lost up to 40% of surface Gal receptor activity and protein. Lost surface receptors were recovered intracellularly with no loss of receptor activity. Type II inhibitors (monensin or chloroquine) induced receptor inactivation but not redistribution. Treated cells lost 50–65% of their surface Gal receptor activity but only ? 15% of their surface receptor protein. These cells lost up to 60% of total cellular Gal receptor activity with no loss of total receptor protein. Of the total inactive Gal receptors, up to 50% and75%, respectively, were present intracellularly in monensin-and chloroquine-treated cells. Loss of ligand binding to permeable treated cells was not due to changes in receptor affinity. A third category, Type III inhibitors (metabolic energy poisons that deplete ATP) induce both Gal receptor redistribution and inactivation (Biochemistry 27:2061, 1988). We conclude that only one of the two previously characterized subpopulations of Gal receptors on hepatocytes, termed State 2 receptors (J Biol Chem 265:629, 1990), recycles constitutively. The activity and distribution of State 2 but not State 1 Gal receptors are differentially affected by these specific drugs or treatments.