Effects of contemporary environment and Quaternary climate change on drylands plant diversity differ between growth forms

Previous studies on large‐scale patterns in plant richness and underlying mechanisms have mostly focused on forests and mountains, while drylands covering most of the world's grasslands and deserts are more poorly investigated for lack of data. Here, we aim to 1) evaluate the plant richness patterns in Inner Asian drylands; 2) compare the relative importance of contemporary environment, historical climate, vegetation changes, and mid‐domain effect (MDE); and 3) explore whether the dominant drivers of species richness differ across growth forms (woody vs herbaceous) and range sizes (common vs rare). Distribution data and growth forms of 13 248 seed plants were compiled from literature and species range sizes were estimated. Generalized linear models and hierarchical partitioning were used to evaluate the relative contribution of different factors. We found that habitat heterogeneity strongly affected both woody and herbaceous species. Precipitation, climate change since the mid‐Holocene and climate seasonality dominated herbaceous richness patterns, while climate change since the Last Glacial Maximum dominated woody richness patterns. Rare species richness was strongly correlated with precipitation, habitat heterogeneity and historical climatic changes, while common species richness was strongly correlated with MDE (woody) or climate seasonality (herbaceous). Temperature had little effects on the species richness patterns of all groups. This study represents the first evaluation of the large‐scale patterns of plant species richness in the Inner Asian drylands. Our results suggest that increasing water deficit due to anthropogenic activities combined with future global warming may increase the extinction risk of many grassland species. Rare species (both herbaceous and woody) may face severe challenges in the future due to increased habitat destruction caused by urbanization and resource exploitation. Overall, our findings indicate that the hypotheses on species richness patterns based on woody plants alone can be insufficient to explain the richness patterns of herbaceous species.     

甲烷氧化过程中铜的作用研究进展

甲烷生物氧化在全球甲烷平衡和温室效应控制中扮演着重要的角色,而铜是甲烷生物氧化过程中的重要影响因子.一方面,铜是调控不同类型甲烷单加氧酶表达的主要影响因子,是组成颗粒性甲烷单加氧酶的必需金属元素;另一方面,在自然环境体系中,铜含量及其形态的变化对甲烷氧化菌的分布、代谢甲烷和非甲烷类有机化合物的能力以及甲烷氧化菌的特异性铜捕获系统也会产生较大影响.准确把握铜在甲烷生物氧化过程中发挥的作用将有助于全面了解甲烷生物氧化过程,进而更好地指导甲烷氧化微生物在温室气体减排及非甲烷有机物污染修复中的应用.本文主要从铜的角度,概述了铜对甲烷氧化菌的分布和活性的影响,介绍了铜在调控甲烷单加氧酶的表达和活性以及调节甲烷氧化菌铜捕获系统方面的作用,并展望了其研究方向.     

植物建植对垃圾填埋场生物覆盖层甲烷氧化及其微生物群落的影响

利用柱试验模拟填埋场生物覆盖层,研究了白三叶和苜蓿建植对增强覆盖层甲烷(CH4)氧化能力及保持甲烷氧化优势菌群的影响。结果表明:植物建植能明显降低基质含水率,提高氮含量,改善O2和CH4扩散,提高基质CH4氧化能力;在CH4氧化的高速期和下降期,植物建植的CH4氧化速率显著高于对照,白三叶和苜蓿处理之间无显著差异;在CH4氧化的低速期,对照与植物建植之间的CH4氧化速率无显著差异,而苜蓿处理显著高于白三叶处理。基于磷脂脂肪酸(PLFA)的微生物群落结构分析表明,植物建植有利于Ⅰ型菌在深层的分布,随着CH4氧化速率逐渐下降,柱体底部甲烷氧化细菌群落由Ⅰ型为主向Ⅱ型为主转变。     

旱地红壤反硝化功能基因丰度对长期施肥的响应

农田施肥会影响土壤微生物驱动的氮素转化和氧化亚氮(N₂O)排放。基于32年的长期肥料定位试验,研究了旱地红壤反硝化功能基因(nirS、nirK、nosZ I和nosZ II)对不同长期施肥处理的响应及其关键影响因素。试验包括6个处理,分别为不施肥(CK)、单施化肥、化肥+花生秸秆、化肥+水稻秸秆、化肥+萝卜菜和化肥+猪粪。结果表明: 与单施化肥相比,化肥和有机物料配施可以有效缓解红壤酸化、提高土壤有机碳含量,其中以化肥和猪粪配施的效果最好。长期施肥对nirK基因丰度没有显著影响,但显著影响nirS基因丰度;与CK相比,长期单施化肥可显著增加nirS基因丰度,增幅达426%,但与单施化肥相比,化肥和有机物料配施降低了nirS基因丰度。旱地红壤中nosZ I基因丰度远高于nosZ II基因丰度,表明nosZ I在酸性红壤中占主导地位;长期施肥对nosZ II基因丰度没有显著影响。但长期施用化肥+猪粪显著提高了nosZ I基因丰度,增幅为138%。逐步回归分析表明,有效磷含量是影响nosZ I基因丰度的关键环境因子,而nosZ II基因丰度则主要受硝态氮含量的影响。化肥和猪粪配施处理的(nirS+nirK)/(nosZ I+nosZ II)值最低,表明化肥和猪粪配施可能会降低旱地红壤的N₂O排放能力。     

Global drivers of population density in terrestrial vertebrates

Aim

Although the effects of life history traits on population density have been investigated widely, how spatial environmental variation influences population density for a large range of organisms and at a broad spatial scale is poorly known. Filling this knowledge gap is crucial for global species management and conservation planning and to understand the potential impact of environmental changes on multiple species.

Location

Global.

Time period

Present.

Major taxa studied

Terrestrial amphibians, reptiles, birds and mammals.

Methods

We collected population density estimates for a range of terrestrial vertebrates, including 364 estimates for amphibians, 850 for reptiles, 5,667 for birds and 7,651 for mammals. We contrasted the importance of life history traits and environmental predictors using mixed models and tested different hypotheses to explain the variation in population density for the four groups. We assessed the predictive accuracy of models through cross‐validation and mapped the partial response of vertebrate population density to environmental variables globally.

Results

Amphibians were more abundant in wet areas with high productivity levels, whereas reptiles showed relatively higher densities in arid areas with low productivity and stable temperatures. The density of birds and mammals was typically high in temperate wet areas with intermediate levels of productivity. The models showed good predictive abilities, with pseudo‐R² ranging between 0.68 (birds) and 0.83 (reptiles).

Main conclusions

Traits determine most of the variation in population density across species, whereas environmental conditions explain the intraspecific variation across populations. Species traits, resource availability and climatic stability have a different influence on the population density of the four groups. These models can be used to predict the average species population density over large areas and be used to explore macroecological patterns and inform conservation analyses.     

Plant presence and species combination, but not diversity, influence denitrifier activity and the composition of nirK-type denitrifier communities in grassland soil

To explore potential links between plant communities, soil denitrifiers and denitrifier function, the impact of presence, diversity (i.e. species richness) and plant combination on nirK -type denitrifier community composition and on denitrifier activity was studied in artificial grassland plant assemblages over two consecutive years. Mesocosms containing zero, four and eight species and different combinations of two species were set up. Differences in denitrifier community composition were analysed by canonical correspondence analyses following terminal restriction fragment length polymorphism analysis of PCR-amplified nirK gene fragments coding for the copper-containing nitrite reductase. As a measure of denitrifier function, denitrifier enzyme activity (DEA) was determined in the soil samples. The presence as well as the combination of plants and sampling time, but not plant diversity, affected the composition of the nirK -type denitrifier community and DEA. Denitrifier activity significantly increased in the presence of plants, especially when they were growing during summer and autumn. Overall, we found a strong and direct linkage of denitrifier community composition and functioning, but also that plants had additional effects on denitrifier function that could not be solely explained by their effects on nirK -type denitrifier community composition.     

Ecophysiology of abundant denitrifying bacteria in activated sludge

The abundance of potential denitrifiers in full-scale wastewater treatment plants with biological nitrogen and phosphorus removal was investigated by FISH and various oligonucleotide probes. The potential denitrifiers were characterized as probe-defined populations that were able to consume radiolabelled substrate with oxygen, nitrate and nitrite as electron acceptor as determined by microautoradiography. The most abundant potential denitrifiers were related to the genera Aquaspirillum, Azoarcus, Thauera and Rhodocyclus, all within the Betaproteobacteria. They made up 20-49% of all bacteria in most of the 17 nitrogen removal plants investigated and were hardly present in four plants without denitrification. The ecophysiology of Aquaspirillum, Azoarcus and Thauera-related bacteria was consistent within each probe-defined group in the plants investigated. These three groups showed distinct physiological differences, with the Aquaspirillum-related bacteria appearing as the most specialized one, consuming only amino acids among the substrates tested, and Thauera as the most versatile consuming some volatile fatty acids, ethanol and amino acids. The coexistence of Aquaspirillum, Azoarcus and Thauera-related bacteria in a range of treatment plants with differences in wastewater, design and operation suggest that the populations ensure a functional stability of the plants by occupying different ecological niches related to the carbon transformation.     

Vertical distribution of nitrite reductase genes (nir S) in continental margin sediments of the Gulf of Mexico

Marine sediments account for up to 66% of the loss of nitrogen load to coastal areas. Sedimentary denitrification is the main sink for fixed nitrogen in the global nitrogen budget, and thus it is important to understand the structure and composition of denitrifying communities. To understand the structure and composition of denitrifying communities, the diversity of nitrite reductase (nirS) genes from sediments along the Gulf of Mexico was examined using a PCR-based cloning approach. Sediments were collected at three different depths (0-0.5, 4-5 and 19-21 cm). Geochemical analysis revealed decreasing nitrate and oxygen concentrations with increasing sediment depth. This trend coincided with the decrease in diversity of denitrifying bacteria. LIBSHUFF analysis indicated that the clone library in the shallowest sediment (depth, 0-0.5 cm) was significantly different from that in the deepest sediment (depth, 19-21 cm), and that the deeper sediments (depths of 4-5 and 19-21 cm) were significantly similar. Community structural shifts were evident between the shallowest (oxic zone) and deepest (anoxic zone) sediments. Community changes within the deepest sediments were more subtle, with the presence of different nirS clone sequences gradually becoming dominant or, alternatively, decreasing with depth. The changes in community structure at this depth are possibly driven by nutrient availability, with lower quality sources of carbon and energy leading to the disappearance of nirS sequences common in the top layer. The majority of recovered nirS sequences were phylogenetically divergent relative to known denitrifying bacteria in the database.     

Trichloroethylene oxidation by the membrane-associated methane monooxygenase in type I,type II and type X methanotrophs

Trichloroethylene (TCE) oxidation was examined in 9 different methanotrophs grown under conditions favoring expression of the membrane associated methane monooxygenase. Depending on the strain, TCE oxidation rates varied from 1 to 677 pmol/min/mg cell protein. Levels of TCE in the reaction mixture were reduced to below 40 nmolar in some strains. Cells incubated in the presence of acetylene, a selective methane monooxygenase inhibitor, did not oxidize TCE.Cultures actively oxidizing TCE were monitored for the presence of the soluble methane monooxygenase (sMMO) and membrane associated enzyme (pMMO). Transmission electron micrographs revealed the cultures always contained the internal membrane systems characteristic of cells expressing the pMMO. Naphthalene oxidation by whole cells, or by the cell free, soluble or membrane fractions was never observed. SDS denaturing gels of the membrane fraction showed the polypeptides associated with the pMMO. Cells exposed to ¹⁴C-acetylene showed one labeled band at 26 kDa, and this protein was observed in the membrane fraction. In the one strain examined by EPR spectroscopy, the membrane fraction of TCE oxidizing cells showed the copper complexes characteristic of the pMMO. Lastly, most of the strains tested showed no hybridization to sMMO gene probes. These findings show that the pMMO is capable of TCE oxidation; although the rates are lower than those observed for the sMMO.     

Potential activity of methane and ammonium oxidation by methanotrophic communities from the soda lakes of southern Transbaikal

Radioisotopic measurements of the methane consumption by mud samples taken from nine Southern Transbaikal soda lakes (pH 9.5–10.6) showed an intense oxidation of methane in the muds of Lakes Khuzhirta, Bulamai Nur, Gorbunka, and Suduntuiskii Torom, with the maximum oxidation rate in the mud of Lake Khuzhirta (33.2 nmol/(ml day)). The incorporation rate of the radioactive label from¹⁴CH₄ into¹⁴CO₂ was higher than into acid-stable metabolites. Optimum pH values for methane oxidation in water samples were 7–8, whereas mud samples exhibited two peaks of methane oxidation activity (at pH 8.15–9.4 and 5.8–6.0). The majority of samples could oxidize ammonium to nitrites; the oxidation was inhibited by methane. The PCR amplification analysis of samples revealed the presence of genes encoding soluble and paniculate methane monooxygenase and methanol dehydrogenase. Three alkaliphilic methanotrophic bacteria of morphotype I were isolated from mud samples in pure cultures, one of which, B5, was able to oxidize ammonium to nitrites at pH 7–11. The data obtained suggest that methanotrophs are widely spread in the soda lakes of Southern Transbaikal, where they can actively oxidize methane and ammonium.     

Spatiotemporal variations in an assemblage of closely related planktonic aerobic methanotrophs

1. The assemblage of aerobic methane‐oxidising bacteria (MOB) was investigated in different seasons in the water column of a stratified freshwater lake. Species composition was analysed by performing denaturing gradient gel electrophoresis (DGGE) of the 16S rRNA genes and cloning analysis of the pmoA gene, which encodes the α‐subunit of particulate methane monooxygenase. The relative abundance of MOB to total bacteria was deduced from the copy number of the pmoA gene and 16S rRNA gene using real‐time polymerase chain reaction. 2. The profiles of the DGGE banding patterns changed with water depth, and these changes correlated with oxygen concentration and water temperature. The sequences of the DGGE bands obtained were all associated with the genus Methylobacter. During the analysis of pmoA gene, all clones sequenced were that of the Methylobacter/Methylosarcina group. The relative abundances of pmoA gene peaked around the oxycline, and small peaks of pmoA gene were also observed near the surface when peaks of methane were observed at the corresponding depth. 3. Profiles of the DGGE banding patterns suggested that ecophysiological characteristics differ among members of the genus Methylobacter; this indicates the importance of investigating the MOB assemblage at the species level or lower. Planktonic MOB seemed to be abundant around oxycline.     

DNA-based analysis of planktonic methanotrophs in a stratified lake

1. The assemblage of planktonic methanotrophs in a stratified freshwater lake was investigated. Vertical patterns were analysed by denaturing gradient gel electrophoresis, using the primer pair specific for 16S rRNA genes of type I methanotrophs.
2. The resulting banding patterns could be divided into three distinct groups, and sequenced bands were all related to the Methylobacter species. No amplicon was obtained with the primer pair specific for type II methanotrophs.
3. Cloning analysis of the pmoA gene was performed using samples from three water depths (epilimnion, metalimnion and hypolimnion). The compositions of the clone libraries from the three depths were distinct from each other but all three libraries were dominated by clones related to Methylobacter species.     

The absolute requirement for carbon dioxide for aerobic methane oxidation by a methanotrophic-heterotrophic soil community of bacteria

An aerobic methanotrophic-heterotrophic soil community has been characterised when growing with different partial pressures of CO₂. The methanotrophic population using methane as carbon source reached 3 × 10⁷ cfu ml^–1 with one of the major methanotrophs being of type II which uses the serine pathway for C assimilation. Optimal methanotrophic activity required the addition of CO₂, and in the absence of CO₂ no methane oxidisers grew. Partial pressures of CO₂ from 1.6 to 11.6 kPa gave optimal cell growth and production of soluble organic compounds. Biomass yield, soluble organics and CO₂ production were 0.36, 0.15, and 0.48 mg mg^–1 methane uptake, respectively, with CO₂ at 11.6 kPa. The results presented here may have important implications for the use of methane-oxidising bacteria in bioremedial applications.