Molecular underpinnings for microbial extracellular electron transfer during biogeochemical cycling of earth elements

Microbial extracellular electron transfer(EET) is electron exchanges between the quinol/quinone pools in microbial cytoplasmic membrane and extracellular substrates. Microorganisms with EET capabilities are widespread in Earth hydrosphere, such as sediments of rivers, lakes and oceans, where they play crucial roles in biogeochemical cycling of key elements, including carbon,nitrogen, sulfur, iron and manganese. Over the past 12 years, significant progress has been made in mechanistic understanding of microbial EET at the molecular level. In this review, we focus on the molecular mechanisms underlying the microbial ability for extracellular redox transformation of iron, direct interspecies electron transfer as well as long distance electron transfer mediated by the cable bacteria in the hydrosphere.     

植物在硅生物地球化学循环过程中的作用

硅是地球上重要的矿质元素,在许多生物地球化学过程中起着重要作用。传统认为硅的循环主要受岩石风化、矿物溶解和水体沉积的影响。实际上,植物在硅的生物地球化学循环中起着重要作用。植物体本身就是一个相当大的硅库,它们能以无定型硅(SiO2.nH2O)的形式积累硅,称作生物硅(BSi)、植硅石或蛋白石。陆地植物每年以BSi的形式固定约1.68×109～5.60×109t的硅,通过枯枝落叶返回到土壤中的BSi有92.5%被植物再吸收,7.5%进入土壤库。陆地植物从土壤BSi库吸收的硅量远超过从岩石风化释放吸收的硅量,植物-土壤内循环的有效性强烈地影响着陆地生态系统中的硅向河流和海洋的输送。在海洋中,硅藻通过吸收、溶解和沉积在很大程度上影响着海洋里的硅循环,硅藻每年固定的硅约为5.60×109～7.84×109t,同样,在向海底沉积的过程中,97%的BSi重新被硅藻吸收,每年只有1.43×108～2.55×108t(约3%)沉积到海底。可见,植物在陆地生态系统和水生生态系统硅的循环中均起着非常重要的作用,研究硅的全球生物地球化学循环时必须考虑到植物的作用。     

Microbial diversity and biogeochemical cycling in soda lakes

Soda lakes contain high concentrations of sodium carbonates resulting in a stable elevated pH, which provide a unique habitat to a rich diversity of haloalkaliphilic bacteria and archaea. Both cultivation-dependent and -independent methods have aided the identification of key processes and genes in the microbially mediated carbon, nitrogen, and sulfur biogeochemical cycles in soda lakes. In order to survive in this extreme environment, haloalkaliphiles have developed various bioenergetic and structural adaptations to maintain pH homeostasis and intracellular osmotic pressure. The cultivation of a handful of strains has led to the isolation of a number of extremozymes, which allow the cell to perform enzymatic reactions at these extreme conditions. These enzymes potentially contribute to biotechnological applications. In addition, microbial species active in the sulfur cycle can be used for sulfur remediation purposes. Future research should combine both innovative culture methods and state-of-the-art ‘meta-omic’ techniques to gain a comprehensive understanding of the microbes that flourish in these extreme environments and the processes they mediate. Coupling the biogeochemical C, N, and S cycles and identifying where each process takes place on a spatial and temporal scale could unravel the interspecies relationships and thereby reveal more about the ecosystem dynamics of these enigmatic extreme environments.     

Non-negligible roles of archaea in coastal carbon biogeochemical cycling

Coastal zones are among the world’s most productive ecosystems. They store vast amounts of organic carbon, as ‘blue carbon’ reservoirs, and impact global climate change. Archaeal communities are integral components of coastal microbiomes but their ecological roles are often overlooked. However, archaeal diversity, metabolism, evolution, and interactions, revealed by recent studies using rapidly developing cutting-edge technologies, place archaea as important players in coastal carbon biogeochemical cycling. We here summarize the latest advances in the understanding of archaeal carbon cycling processes in coastal ecosystems, specifically, archaeal involvement in CO₂ fixation, organic biopolymer transformation, and methane metabolism. We also showcase the potential to use of archaeal communities to increase carbon sequestration and reduce methane production, with implications for mitigating climate change.     

A hierarchical approach to evaluating the significance of soil biodiversity to biogeochemical cycling

The significance of biodiversity to biogeochemical cycling is viewed most directly through the specific biogeochemical transformations that organisms perform. Although functional diversity in soils can be great, it is exceeded to a high degree by the richness of soil species. It is generally inferred from this richness that soil systems have a high level of functional redundancy. As such, indices of species richness probably contribute little to understanding the functioning of soil ecosystems. Another approach stresses the value of identifying keystone organisms, that is those that play an exceptionally important role in determining the structure and function of ecosystems. Both views tend to ignore the importance of biodiversity in maintaining the numerous and complex interactions among organisms in soils and their contributions to biogeochemical cycling. We describe some of those interactions and their importance to ecosystem function.Soil organisms alter the physical, chemical and biological properties of soils in innumerable ways. The composition and structure of biotic communities at one hierarchical level can influence the spatial heterogeneity of resource and refuge patches at other hierarchical levels. This spatial heterogeneity is supported by a number of biologically relevant spheres of influence that include the detritusphere, the drilosphere, the porosphere, the aggregatusphere and the rhizosphere. Each has fairly distinct properties that operate at different spatial scales. We discuss how these properties may function in regulating the interactions among organisms and the biogeochemical processes that they mediate. It is through the formation of a spatially and temporally heterogeneous structure that biodiversity may contribute most significantly to the functioning of soil ecosystems. Real advances in understanding the significance of biodiversity to biogeochemical cycling will come from taking a broader view of biodiversity. Such a view will necessarily encompass many levels of resolution including: 1) the importance of biodiversity to specific biogenic transformations, 2) the complexity and specificity of biotic interactions in soils that regulate biogeochemical cycling, and 3) how biodiversity may operate at different hierarchically arranged spatial and temporal scales to influence the structure and function of ecosystems.     

Enzymes and biogeochemical cycling in wetlands during a simulated drought

Possible interactions between soil enzymes and thebiogeochemistry of wetlands were investigated duringa field-based drought simulation. Under control(waterlogged) conditions, correlations were foundbetween the activity of the enzyme B-glucosidase andtwo properties associated with carbon cycling, namelyi) CH₄ release r = 0.79,p lt 0.01) and ii) dissolvedorganic carbon concentration (r= -0.81, p lt 0.01). In contrast,the transition to drought conditions resulted in correlations betweenB-glucosidase activity and certain mineralisationprocesses, namely the release of mg and Ca(r = 0.72, p lt 0.05). Sulphataseactivity correlated with changes in sulphate concentration during the droughtsimulation (r = 0.73, p lt 0.05).Further support for the suggested enzymic involvement in biogeochemicalprocesses was found in laboratory studies. Theseexperiments indicated that increasing the abundance ofB-glucosidase could stimulate trace gas emissions(p lt 0.001) and increase the concentration ofmagnesium and calcium (p lt 0.05). Increasedsulphatase abundance caused a suppression of methane emissions(p = 0.053).     

Molecular approaches to malaria

Malaria is a serious health problem in developing countries. With the complete sequencing of the genomes of the parasite and of the mosquito vector, malaria research has entered the post-genome era. In this report we summarize the results and new research avenues presented at a recent meeting held with the aim of developing interdisciplinary approaches to combat this disease.     

Some thoughts on the biogeochemical cycling of potassium in terrestrial ecosystems

Biogeochemistry - Potassium presents a conundrum for biogeochemists. Potassium is cycled wastefully at the plant level, but it appears to be conserved in the nutrient budgets of entire ecosystems,...     

Carbon and nitrogen biogeochemical cycling potentials of supraglacial cryoconite communities

Microorganisms have a crucial role to play in the cycling of nutrients within glacial environments. These systems are often nutrient-limited, and so biogeochemical reactions, which ensure the availability of nutrients for microbial communities, are critical for the maintenance of these systems. This study uses molecular biology to characterise the supraglacial cryoconite microbial communities that are capable of cycling carbon and nitrogen in a range of glacial environments. Organisms with the potential to photosynthesise were identified, including Cyanobacteria, Actinobacteria, Betaproteobacteria, Stramenopiles and Haptophyceae. Organisms with the potential to perform nitrification and denitrification processes were also identified and featured Betaproteobacteria, Alphaproteobacteria, Thaumarchaeota and Cyanobacteria. While it is unlikely that the chemical and physical parameters of the supraglacial environment will facilitate optimal rates of all of the nitrogen-related biogeochemical processes, the transport of these cryoconite communities to downstream locations, where more favourable conditions may prevail, will perhaps provide a valuable inoculation of microorganisms with the genetic potential to catalyse these reactions elsewhere.     

微生物参与海草床元素循环及其生态修复功能

海草是分布在全球海岸带的沉水被子植物,与周围环境共同形成的海草床生态系统是三大典型海洋生态系统之一,具有十分重要的生态功能。20世纪以来,全球海草床衰退严重,研究海草床的生态修复迫在眉睫,现有修复方法未能足够重视微生物在海草床中的重要作用。本文综合阐述了微生物在海草床生态系统有机物矿化和营养流动过程中起到的作用,分析了微生物驱动下的海草床水体与沉积物之间的元素循环,提出了人类活动引起海草床退化的原因,总结了海草床微生物的系统研究方法,并在此基础上提出从微生物生态的角度修复海草床的新思路。     

An introduction to the biogeochemical cycling of calcium and substitutive strontium in living coral reef mesocosms

The coral reef mesocosms designed by the Smithsonian Institution's Dr. Walter Adey, his Marine System Laboratory personnel, and staff members of the Pittsburgh Aqua-Zoo simulate most of the physical, chemical, and biological parameters found in natural Caribbean coral reefs. After developing the mesocosm in Pittsburgh, an evaluation and comparison between natural reef seawater sources and closed mesocosm seawater conditions indicated that an additional parameter should be investigated. It was hypothesized that, given time, the aragonite- and calcite (CaCO₃ crystal forms)-producing organisms in the closed mesocosms could deplete the seawater of available Ca²⁺ and substitutive Sr²⁺. Atomic absorption spectrophotometry was utilized to determine concentrations in the seawater over time. Results showed a substantial reduction in dissolved Ca and Sr in the mesocosm after approximately two years. Dissolved aragonitic Halimeda algae parts were put into the system for replacive purposes. In terms of the biogeochemical cycling of Ca²⁺ and Sr²⁺, the coral reef mesocosm organisms behaved similarly to natural reefs, which have a constant supply of dissolved Ca²⁺ and Sr²⁺. Further research utilizing radiolabeled sources of Ca²⁺, Sr²⁺, and Mg²⁺, in conjunction with in vivo scanning electron microscopy (SEM) and growth increment studies, are recommended for determining the exact biogeochemical pathways for these elements in coral reefs, and to quantify growth parameters. © 1993 Wiley-Liss, Inc.     

Molecular approaches to nontoxic antifouling

Summary

A consequence of environmental and human health concerns arising from the use of toxic metals in marine antifouling coatings has been to recognise the need for a nontoxic alternative to fouling control. Recent research has focused on two approaches to this problem: the development of (a) foul-release coatings that work on the principle of either low surface free energy or coating ablation, and (b) coatings that incorporate a compound(s) that is nontoxic, or at least environmentally benign, that will deter fouling. Here we discuss the nature of the fouling problem and a new technology that is emerging to address it. The use of natural marine products and of analogues to these compounds holds considerable promise and is an area of intense research. It is recognized, however, that a melding of the technologies of foul-release and foul-deterrence may be required to develop broad spectrum, nontoxic antifouling coatings. This approach may more closely reflect antifouling strategies adopted by marine organisms that maintain a foul-free surface.     

Molecular approaches to contraceptive development

The next generation of contraceptives will be based on the identification of novel molecules essential for reproductive processes and will rely on the refinement of older as well as newer technologies. Functional analysis of naturally occurring reproductive genetic disorders and creation of mice null for specific genes would greatly assist in the choice of genetic targets for contraceptive development. Structure-based design of drugs as exemplified by the preparation of an orally active non-peptide gonadotropin releasing hormone (GnRH) would revolutionize drug formulation and delivery for a peptide analogue. This review examines some of the molecular targets that may change contraceptive choices in the future.     

Archaea in metazoan diets: implications for food webs and biogeochemical cycling

Although the importance of trophic linkages, including ‘top-down forcing'', on energy flow and ecosystem productivity is recognized, the influence of metazoan grazing on Archaea and the biogeochemical processes that they mediate is unknown. Here, we test if: (1) Archaea provide a food source sufficient to allow metazoan fauna to complete their life cycle; (2) neutral lipid biomarkers (including crocetane) can be used to identify Archaea consumers; and (3) archaeal aggregates are a dietary source for methane seep metazoans. In the laboratory, we demonstrated that a dorvilleid polychaete, Ophryotrocha labronica, can complete its life cycle on two strains of Euryarchaeota with the same growth rate as when fed bacterial and eukaryotic food. Archaea were therefore confirmed as a digestible and nutritious food source sufficient to sustain metazoan populations. Both strains of Euryarchaeota used as food sources had unique lipids that were not incorporated into O. labronica tissues. At methane seeps, sulfate-reducing bacteria that form aggregations and live syntrophically with anaerobic-methane oxidizing Archaea contain isotopically and structurally unique fatty acids (FAs). These biomarkers were incorporated into tissues of an endolithofaunal dorvilleid polychaete species from Costa Rica (mean bulk δ¹³C=−92±4‰ polar lipids −116‰) documenting consumption of archaeal-bacterial aggregates. FA composition of additional soft-sediment methane seep species from Oregon and California provided evidence that consumption of archaeal-bacterial aggregates is widespread at methane seeps. This work is the first to show that Archaea are consumed by heterotrophic metazoans, a trophic process we coin as ‘archivory''.