Microbial carbon limitation: The need for integrating microorganisms into our understanding of ecosystem carbon cycling

Numerous studies have demonstrated that fertilization with nutrients such as nitrogen, phosphorus, and potassium increases plant productivity in both natural and managed ecosystems, demonstrating that primary productivity is nutrient limited in most terrestrial ecosystems. In contrast, it has been demonstrated that heterotrophic microbial communities in soil are primarily limited by organic carbon or energy. While this concept of contrasting limitations, that is, microbial carbon and plant nutrient limitation, is based on strong evidence that we review in this paper, it is often ignored in discussions of ecosystem response to global environment changes. The plant‐centric perspective has equated plant nutrient limitations with those of whole ecosystems, thereby ignoring the important role of the heterotrophs responsible for soil decomposition in driving ecosystem carbon storage. To truly integrate carbon and nutrient cycles in ecosystem science, we must account for the fact that while plant productivity may be nutrient limited, the secondary productivity by heterotrophic communities is inherently carbon limited. Ecosystem carbon cycling integrates the independent physiological responses of its individual components, as well as tightly coupled exchanges between autotrophs and heterotrophs. To the extent that the interacting autotrophic and heterotrophic processes are controlled by organisms that are limited by nutrient versus carbon accessibility, respectively, we propose that ecosystems by definition cannot be ‘limited’ by nutrients or carbon alone. Here, we outline how models aimed at predicting non‐steady state ecosystem responses over time can benefit from dissecting ecosystems into the organismal components and their inherent limitations to better represent plant–microbe interactions in coupled carbon and nutrient models.     

Biodiesel production via transesterification of palm olein using waste mud crab (Scylla serrata) shell as a heterogeneous catalyst

A recent rise in crab aquaculture activities has intensified the generation of waste shells. In the present study, the waste shells were utilized as a source of calcium oxide to transesterify palm olein into methyl esters (biodiesel). Characterization results revealed that the main component of the shell is calcium carbonate which transformed into calcium oxide when activated above 700 °C for 2 h. Parametric studies have been investigated and optimal conditions were found to be methanol/oil mass ratio, 0.5:1; catalyst amount, 5 wt.%; reaction temperature, 65 °C; and a stirring rate of 500 rpm. The waste catalyst performs equally well as laboratory CaO, thus creating another low-cost catalyst source for producing biodiesel. Reusability results confirmed that the prepared catalyst is able to be reemployed up to 11 times. Statistical analysis has been performed using a Central Composite Design to evaluate the contribution and performance of the parameters on biodiesel purity.     

A simple technique for producing 13C or 14C-labelled fronds of Lemna gibba and their use in soil incubation investigations

The duckweed Lemna gibba required light and a suitable energy source such as sucrose, glucose or fructose, for maximum growth in culture. The requirement for light was relatively unimportant and the plants grew well in a photon flux density of only 52 μmol m^-2s^-1 PAR. The uptake and incorporation of uniformly labelled ¹⁴C-glucose into fronds was related only to the concentration of the sugar. When incubated with soil, labelled L. gibba behaved in a manner similar to that of labelled ryegrass roots which had been produced by a more elaborate technique using a ¹⁴CO₂ labelled atmosphere. During incubation with soil for 224 days the L. gibba material (specific activity 6133 Bq mg^-1 d. wt) lost 64% of its radioactivity as ¹⁴CO₂ and ryegrass (specific activity 6634 Bq mg^-1 d. wt) lost 49%. Alkaline extracted humic and fulvic acids from soil had specific activities for the L. gibba incubation of 3409 and 407 Bq mg^-1 solid and for ryegrass roots of 4609 and 546 Bq mg^-1 solid respectively. The production of ¹³C or ¹⁴C-labelled L. gibba can be undertaken using only simple equipment producing material the specific radioactivity of which can be controlled by adjusting the activity of the sugar energy source.     

西沙永兴岛抗风桐与海岸桐群落凋落叶分解及中型土壤动物的贡献

我国南海诸岛主要是珊瑚岛。植物凋落物分解是生态系统元素循环的关键环节,但目前关于南海珊瑚岛生态系统凋落物分解的研究还是空白。以我国西沙群岛的优势树种抗风桐（Pisonia grandis）和海岸桐（Guettarda speciosa）为研究对象,采用凋落物袋法,分别于分解期间的第3、6、9、13和15个月取样,探究中型土壤动物对两种植物群落中凋落物分解过程中质量损失和养分释放的影响。结果表明：与没有中型土壤动物存在的情况（0.1 mm凋落物袋）相比,分解开始后的6个月内,中型土壤动物存在（2 mm凋落物袋）使抗风桐和海岸桐凋落叶分解速率分别提高了12.3%和4.8%（P<0.05）;分解6-15个月期间,中型土壤动物存在使抗风桐和海岸桐凋落叶分解速率分别提高了33.0%和12.3%（P<0.05）。中型土壤动物排除显著影响了不同分解阶段凋落叶总碳（Total carbon,TC）、总氮（Total nitrogen,TN）、纤维素、木质素和半纤维素的残留率变化。中型土壤动物群落组成受土壤温度显著影响（P<0.05）,它们对凋落叶分解的贡献可能主要受优势类群如真螨目和寄螨目的影响。相较海岸桐,抗风桐凋落叶的分解周期更短,中型土壤动物对其的贡献更大;选用抗风桐作为南海珊瑚岛退化植被恢复或新建的先锋种对促进生态系统元素循环更有利。     

The influence of locus number and information content on species delimitation: an empirical test case in an endangered Mexican salamander

Perhaps the most important recent advance in species delimitation has been the development of model‐based approaches to objectively diagnose species diversity from genetic data. Additionally, the growing accessibility of next‐generation sequence data sets provides powerful insights into genome‐wide patterns of divergence during speciation. However, applying complex models to large data sets is time‐consuming and computationally costly, requiring careful consideration of the influence of both individual and population sampling, as well as the number and informativeness of loci on species delimitation conclusions. Here, we investigated how locus number and information content affect species delimitation results for an endangered Mexican salamander species, Ambystoma ordinarium. We compared results for an eight‐locus, 137‐individual data set and an 89‐locus, seven‐individual data set. For both data sets, we used species discovery methods to define delimitation models and species validation methods to rigorously test these hypotheses. We also used integrated demographic model selection tools to choose among delimitation models, while accounting for gene flow. Our results indicate that while cryptic lineages may be delimited with relatively few loci, sampling larger numbers of loci may be required to ensure that enough informative loci are available to accurately identify and validate shallow‐scale divergences. These analyses highlight the importance of striking a balance between dense sampling of loci and individuals, particularly in shallowly diverged lineages. They also suggest the presence of a currently unrecognized, endangered species in the western part of A. ordinarium's range.     

青冈林土壤跳虫群落结构在落叶分解过程中的变化

1993年5月至1995年4月,用落叶代法研究青冈（Cyclobalanopsis glauca）落叶分解过程中跳虫的群落结构变化。用多样性指数、演替指数、相似系数分析跳虫在落叶分解过程中群落结构及其季节变化特点。青冈落叶分解经淋洗、养分固定 养分活化3个阶段,分解常数分别为k1=9.11,k2=2.57,k3=0.43（百分比／月）。跳中心在落叶分解过程中的集聚型分为3组：A组为落叶分解前期集聚的种类,B组为后期的种类,C组为中期或全过程的种类,分析讨论了落叶分解过程与跳虫功能群及群落结构变化的关系。     

Nitrogen availability affects saprotrophic basidiomycetes decomposing pine needles in a long term laboratory study

Fungi, especially basidiomycetous litter decomposers, are pivotal to the turnover of soil organic matter in forest soils. Many litter decomposing fungi have a well-developed capacity to translocate resources in their mycelia, a feature that may significantly affect carbon (C) and nitrogen (N) dynamics in decomposing litter. In an eight-month long laboratory study we investigated how the external availability of N affected the decomposition of Scots pine needles, fungal biomass production, N retention and N-mineralization by two litter decomposing fungi – Marasmius androsaceus and Mycena epipterygia. Glycine additions had a general, positive effect on fungal biomass production and increased accumulated needle mass loss after 8 months, suggesting that low N availability may limit fungal growth and activity in decomposing pine litter. Changes in the needle N pool reflected the dynamics of the fungal mycelium. During late decomposition stages, redistribution of mycelium and N out from the decomposed needles was observed for M. epipterygia, suggesting autophagous self degradation.     

Early-stage litter decomposition and its influencing factors in the wetland of the Sanjiang Plain, China

Using the litter bag technique, the decomposition rates and their influencing factors were studied by investigating three wetland macrophytes, Calamagrostics angustifolia, Carex meyeriana and Carex lasiocapa, in Sanjiang Plain, Northeast China. It was revealed that C. lasiocapa lost 28.91% of its weight, C. angustifolia lost 31.98% and C. meyeriana lost 32.99% after 164 days. Another finding was that the amount of organic carbon in the litter of C. angustifolia and C. lasiocapa fluctuated, but continuously decreased in that of C. meyeriana. However, all the three types of litter released organic carbon. Nitrogen was released substantially from the litter of both C. angustifolia and C. meyeriana, but accumulated in the litter of C. lasiocapa. Phosphorus concentrations in all the three types of litter apparently decreased first and then slightly increased. Overall, P release was observed in all the three types of litter. The C/N and C/P ratios varied significantly in the decomposition process. The decomposition rates and nutrient content variations were simultaneously influenced by the quality of the litter as well as the environmental factors in the Sanjian Plain, but they were more strongly affected by the quality of the litter.     

外源氮素添加对森林土壤氨基糖转化的影响

采用室内模拟培养法研究了不同数量氮素添加条件下森林土壤中3种微生物来源的氨基糖含量的动态变化,并且利用氨基葡萄糖和胞壁酸的比值分析了氮素添加条件下土壤真菌和细菌对土壤氮素转化和积累的相对贡献。结果表明:土壤中氨基糖含量的动态变化与土壤中的养分状况密切相关;当向土壤中添加氮源时,微生物会利用外加氮源合成自身的细胞壁物质,并且高氮处理胞壁酸含量高于低氮处理,而高氮处理氨基葡萄糖含量则低于低氮处理,说明随施氮量的增加更有利于以胞壁酸为代表的细菌残留物在土壤中的积累,不利于以氨基葡萄糖为代表的真菌残留物的积累,氨基半乳糖对氮素添加的响应较小;当土壤中养分缺乏时,氨基糖能够发生不同程度的分解;添加氮源条件下,真菌和细菌来源氨基糖的比值发生变化,细菌对土壤氮素转化的贡献大于真菌,并且高氮处理细菌的贡献更大。本研究表明,氮素添加改变了以氨基糖为代表的土壤氮素的微生物转化过程。     

Differential parameters between cytosolic 2‐Cys peroxiredoxins,PRDX1 and PRDX2

Peroxiredoxins are thiol‐dependent peroxidases that function in peroxide detoxification and H₂O₂ induced signaling. Among the six isoforms expressed in humans, PRDX1 and PRDX2 share 97% sequence similarity, 77% sequence identity including the active site, subcellular localization (cytosolic) but they hold different biological functions albeit associated with their peroxidase activity. Using recombinant human PRDX1 and PRDX2, the kinetics of oxidation and hyperoxidation with H₂O₂ and peroxynitrite were followed by intrinsic fluorescence. At pH 7.4, the peroxidatic cysteine of both isoforms reacts nearly tenfold faster with H₂O₂ than with peroxynitrite, and both reactions are orders of magnitude faster than with most protein thiols. For both isoforms, the sulfenic acids formed are in turn oxidized by H₂O₂ with rate constants of ca 2 × 10³ M^?1 s^?1 and by peroxynitrous acid significantly faster. As previously observed, a crucial difference between PRDX1 and PRDX2 is on the resolution step of the catalytic cycle, the rate of disulfide formation (11 s^?1 for PRDX1, 0.2 s^?1 for PRDX2, independent of the oxidant) which correlates with their different sensitivity to hyperoxidation. This kinetic pause opens different pathways on redox signaling for these isoforms. The longer lifetime of PRDX2 sulfenic acid allows it to react with other protein thiols to translate the signal via an intermediate mixed disulfide (involving its peroxidatic cysteine), whereas PRDX1 continues the cycle forming disulfide involving its resolving cysteine to function as a redox relay. In addition, the presence of C83 on PRDX1 imparts a difference on peroxidase activity upon peroxynitrite exposure that needs further study.