Important Biogeochemical Cycles Research Articles

Pseudodesulfovibrio pelocollis sp. nov. a Sulfate-Reducing Bacterium Isolated from a Terrestrial Mud Volcano.

Terrestrial mud volcanoes (TMVs), surface expressions of a deep-subterranean sedimentary volcanism, are widespread throughout the world. The methane and sulfur cycles are recognized as the most important biogeochemical cycles in these environments. Only few anaerobic bacterial strains were recovered from TMVs. We have isolated a novel sulfate-reducing bacterium (strain SB368T) from TMV located at Taman Peninsula, Russia. Optimum growth of strain SB368T was observed at 30°C, pH 8.0 and 1% NaCl. Strain SB368T utilized lactate, pyruvate and fumarate in the presence of sulfate, sulfite or thiosulfate. Growth with molecular hydrogen was observed only in the presence of acetate. Fermentative growth occurred on pyruvate. Phylogenetic analysis revealed that strain SB368T belongs to the genus Pseudodesulfovibrio but is distinct from all described species. Based on its genomic and phenotypic properties, a new species, Pseudodesulfovibrio pelocollis sp. nov. is proposed with strain SB368T (= DSM 111087T = VKM B-3585T) as a type strain.

Nitrate-Reducing Fe(II)-Oxidizing microorganisms: linking Fe, C and N Cycles in subsurface environments

The discovery of the Nitrate-Reducing Fe(II)-Oxidizing (NRFeOx) microbial metabolism, which couples the oxidation of Fe(II) to the reduction of nitrate (NO3-) using organic matter or carbon dioxide (CO2) as carbon source, was a major milestone in microbial ecology (Straub et al. 1996). NRFeOx microorganisms play an essential role on a global scale in three of the most important biogeochemical cycles: iron (Fe), carbon (C) and nitrogen (N) (Kappler et al. 2021, Huang et al. 2021). In addition, these organisms participate in the mobilization or stabilization of organic carbon, as well as in CO2 fixation, thus contributing to the reduction of atmospheric CO2 (Kappler et al. 2021). Finally, the activity of these microorganisms is key to remove the pollutant NO3- from aquifers, which is one of the major worldwide environmental issues since many environments exceed the maximum regulatory concentration (50 mg L-1) (Kazakis et al. 2020 ). A plethora of NRFeOx microorganisms have been described in the last decades. However, most of these microorganisms have been reclassified as chemodenitrifiers. That is to say, Fe(II) is not enzymatically oxidized but indirectly by the reactive nitrogen species produced during denitrification (Fig. 1 ). In fact, only in three cultures so far, named KS, BP and AG, has the presence of true NRFeOx metabolism been unequivocally demonstrated (Straub et al. 1996, Huang et al. 2021b, Jakus et al. 2021b). Cultures KS, BP and AG have been studied thoroughly in the past years, analyzing the rate and mechanism by which these communities carry out autotrophic NRFeOx. Different omics studies have revealed that cultures KS, BP and AG consist of a mixture of bacterial species, which collaborate in order to grow under autotrophic NRFeOx conditions. Each culture is dominated by a novel candidate species of the genus Ferrigenium (Huang et al. 2022) capable of fixing CO2 and oxidizing Fe(II), but which requires flanking species to complete denitrification (Huang et al. 2021b, He et al. 2016, Huang et al. 2021a). Interestingly, these communities not only carry out NRFeOx using dissolved Fe(II) as energy source (Straub et al. 1996, Huang et al. 2021b, Jakus et al. 2021b), but they can also oxidize Fe(II) minerals, the main form in which Fe(II) can be found in the Earth's crust (Huang et al. 2021). In fact, Fe(II)-bearing minerals are thought to be the main drivers of NO3- reduction in subterranean environments (Huang et al. 2021), which has additional ecological consequences. NRFeOx microorganisms can trigger the turnover of the Fe(II)-bearing minerals, resulting in the mobilization of mineral structural elements such as S, P, C or contaminant heavy metals and the precipitation of Fe(III) minerals at circumneutral pH (Weber et al. 2001, Jakus et al. 2021a). Here, we will present a review of the insights learned from the three NRFeOx autotrophic cultures and discuss their ecological role, their importance in biogeochemical cycles, and their potential biotechnological applications.

Characterization of pollutants and identification of microbial communities in the filter media of green infrastructures

Green infrastructure (GI) technologies use natural mechanisms and processes associated with microorganisms, plants, and filter media to facilitate mass circulation and energy flow in the ecosystem. Despite the numerous studies focused on the functions and pollutant treatment performance of nature-based stormwater treatment technologies, studies concerning the effects of filter media characteristics on the diversity and abundance of microorganisms in green stormwater infrastructures are still lacking. In this study, the physico-chemical characteristics of filter media and accumulated sediments in an infiltration trench (IT) and bioretention facility (BI) were investigated. Moreover, the composition and distribution of different microbial communities in GIs designed for stormwater treatment were identified. As compared with BI, higher pollutant concentrations were noted on the filter media and sediments accumulated in IT due to the higher degree of anthropogenic activities in IT's catchment area. Inorganic filter media (i.e., gravel) tend to have greater pollutant trapping efficiency due to the accumulation of sediments in the macropores. On the other hand, organic filter materials (i.e., woodchips) may serve as carbon sources for fueling microbial processes and promote better moisture retention in the facility. Proteobacteria, which constituted 38.6% to 43.0% of the total bacterial population in IT and 37.9% to 41.4% of the total bacterial population in BI, was found to be the most dominant type of bacteria in the facilities. In terms of microbial diversity, BI exhibited a higher diversity index, which is most likely due to the presence of vegetative components forming a symbiotic relationship with microbial colonies. Generally, inorganic filter media are mainly used for improving the GI technologies' drainage and infiltration functions, whereas organic filter media provide suitable growth environments for different bacterial communities involved in important biogeochemical cycles.

Addressing the Relationship between Leaf Nitrogen and Carbon Isotope Discrimination from the Three Levels of Community, Population and Individual.

The carbon, nitrogen and water cycles of terrestrial ecosystems are important biogeochemical cycles. Addressing the relationship of leaf nitrogen (N) and carbon isotope discrimination (Δ) will enhance the understanding of the links between these three cycles in plant leaves because Δ can reflect time-integrated leaf-level water-use efficiency (WUE) over the period when the leaf material is produced. Previous studies have paid considerable attention to the relationship. However, these studies have not effectively eliminated the interference of environmental factors, inter-species, and inter-individual differences in this relationship, so new research is necessary. To minimize these interferences, the present work explored the relationship at the three levels of community, population, and plant individual. Three patterns of positive, negative and no relationship were observed across communities, populations, and individuals, which is dependent on environmental conditions, species, and plant individuals. The results strongly suggested that there is no general pattern for the relationship between leaf N and Δ. Furthermore, the results indicated that there is often no coupling between leaf-level long-term WUE and leaf N in the metabolic process of carbon, N and water in leaves. The main reason for the lack of this relationship is that most plants do not invest large amounts of nitrogen into photosynthesis. In addition, the present study also observed that, for most plant species, leaf N was not related to photosynthetic rate, and that variations in photosynthetic rates are mainly driven by stomatal conductance.

Microbial iron cycling is prevalent in water-logged Alaskan Arctic tundra habitats, but sensitive to disturbance.

Water logged habitats in continuous permafrost regions provide extensive oxic-anoxic interface habitats for iron cycling. The iron cycle interacts with the methane and phosphorus cycles, and is an important part of tundra biogeochemistry. Our objective was to characterize microbial communities associated with the iron cycle within natural and disturbed habitats of the Alaskan Arctic tundra. We sampled aquatic habitats within natural, undisturbed and anthropogenically disturbed areas and sequenced the 16S rRNA gene to describe the microbial communities, then supported these results with process rate and geochemical measurements. Undisturbed habitats have microbial communities that are significantly different than disturbed habitats. Microbial taxa known to participate in the iron and methane cycles are significantly associated with natural habitats, whereas they are not significantly associated with disturbed sites. Undisturbed habitats have significantly higher extractable iron and are more acidic than disturbed habitats sampled. Iron reduction is not measurable in disturbed aquatic habitats and is not stimulated by the addition of biogenic iron mats. Our study highlights the prevalence of Fe-cycling in undisturbed water-logged habitats, and demonstrates that anthropogenic disturbance of the tundra, due to legacy gravel mining, alters the microbiology of aquatic habitats and disrupts important biogeochemical cycles in the Arctic tundra.

Prospect of Ru(edta) complexes in nitrogen cycle electrocatalysis: a mini review

This mini review chronicles the role of Ru(edta) (edta4− = ethylenediaminetetraacetate) towards catalysing the electrochemical transformation of nitrogen cycle reactions, elucidating the complex mechanistic schemes.

Editorial

三峡工程举世瞩目，是长江流域大保护与流域水安全保障的关键性枢纽工程。自2003年三峡工程蓄水以来，在防洪、发电、航运、供水等方面产生了巨大的经济、社会及生态环境等综合效益。同时，水库建成后，重庆至宜昌600多km的自然河道变成了人为控制的大型河流型深水水库，不仅在库区形成了诸如消落带、干-支流往复交融的独特生境，而且由于下泄水流、泥沙、营养盐等水文及生物地球化学要素的时空变化，长江中、下游河床冲淤及演变均出现了一些新特征，江-湖关系也变得比2003年之前更加错综复杂，长江流域迎来了“后三峡工程”时代。为了阶段性系统总结、交流这20年来三峡水库生态环境效应研究的成果，《湖泊科学》编辑委员会特邀我们组织了本专辑。自2022年4月发布征稿启示以来，先后收到各类来稿60余篇，经过多轮审稿，最终25篇得以录用发表。 专辑不少研究成果都数据翔实、针对性强，体现了当下我国三峡工程生态环境效应研究的水平。(1)在水文水资源方面，不仅总结了长江中下游干流及两湖的径流泥沙变化，而且研究改进了三峡入库洪水概率预报方法，尤其是针对工程运用后三峡水库泥沙淤积及长江中下游河床调整、河道冲刷、航道水深资源等方面更是有多篇论文刊发。(2)在水环境水生态方面，对水动力、水沙变化引起的生态环境效应进行了系统的归纳和分析，并对水库消落带土壤-植物-微生物作用下的氮循环关键过程研究进行了系统回顾；研究认为，目前的水库富营养化及潜在的水华风险主要在支流，但是对干、支流浮游植物生长增殖的因果响应也要积极关注。(3)在流域生物多样性保育方面，专辑重点关注了消落区植物群落演变及优势植物适应策略、后三峡工程时代的鄱阳湖湿地植被生产力演变以及水库库尾江段产漂流性卵鱼类早期资源等。(4)在流域水安全方面，有论文针对库湾水-气界面热交换过程及水体稳定性进行了分析；我们高兴的发现，模拟分析揭示了三峡水库成库以来的气候效应主要集中在局地和近地层，而不是区域性的，这一研究成果无疑具有积极和深远的意义。(5)作为我国最大的水库，其温室气体排放及对“碳中和”“碳达峰”的贡献研究，无疑也引起了国内外学者的积极和长期关注，专辑中对水库CO2、CH4通量监测分析研究进行了系统回顾与展望，这也将是未来三峡水库的研究热点之一。 这是《湖泊科学》近10年来策划出版的第4个专辑。专辑不在多而在于精，未来我们还将持续关注三峡水库，长期跟踪、重点报道后三峡工程时代长江流域水资源、水生态、水环境、水安全方面的研究成果，更好的为长江大保护和我国水生态文明建设服务。;The Three Gorges Project is a key pivotal hydro-project in the Yangtze River Basin for the protection and security of water resources, which has been attracting worldwide attention over the past decades. Since the impoundment of the Three Gorges Reservoir in 2003, the project has created great economic, social, and ecological benefits in terms of flood control, hydropower generation, navigation, and water supply. Meanwhile, the reservoir formation has drastically transformed the 600km natural river reach of Yangtze, from Chongqing to Yichang, to a large river-valley dammed reservoir with deep water regulated by the dam. Such has created unique landscapes and habitats within the reservoir, e.g., drawdown area along the shorelines, reciprocal fluctuating backwater water area between tributaries and the main stem, etc. In addition, the regulation of the reservoir discharge also leads to new patterns of spatiotemporal variations of hydrological and biogeochemical parameters, e.g., sediment transport, fluvial equilibrium of downstream channels, nutrient exports, etc. The river-lake relationships in the mid and lower reach of the Yangtze have been becoming more complex than before 2003. The Yangtze River basin is now in a post-Three-Gorges-Project era. To summarize the state of research on the ecological and environmental effects caused by the Three Gorges Reservoir in the past 20 years, the editorial board of the Journal of Lake Sciences invited us to organize this special issue. The call for papers was announced in April 2022. Since then, more than 60 manuscripts have been received, and after extensive reviews, 25 of them were finally accepted for publication. The manuscripts collected in the special issue are informative and relevant, representing the knowledge-of-the-art of the ecological and environmental effects of the giant hydro-project in history. (1) In the area of hydrology and water resources, sediment transport in the mid and lower reaches of the Yangtze, as well as their exchange with the Dongting Lake and Poyang Lake, were elaborated. The special issue also collected novel methodologies for the flood prediction of the reservoir inflow, in particular, the fluctuation of a downstream riverbed after the operation of the Three Gorges Reservoir, as well as the situation of river scouring and channel depth variation, were extensively discussed. (2) In the area of water environment and aquatic ecology, the special issue systematically addressed the ecological and environmental effects caused by hydrological and hydrodynamic conditions. The important biogeochemical cycles of nitrogen within the soil-plant-microbial interactions in the reservoir drawdown area were also reviewed and discussed profoundly. It highlighted the tributaries of the Yangtze in the reservoir, exhibiting the trends of eutrophication, had potential risks of algal blooms. However, the causal chain of phytoplankton growth in the main stem and tributaries should also be taken into further attention. (3) In the area of watershed biodiversity conservation, the special issue collected manuscripts on the evolution of vegetation communities and adaptive strategies of dominant populations in the drawdown area. The evolution of vegetation productivity in the wetland of Poyang Lake was discussed. The research on drifting egg-producing fish populations was also included in the special issue. (4). In the watershed water security, manuscripts in the special issue discussed the air-water heat transfer process and thermal stability of the water column in the reservoir. Rather than regionally, we were delighted to find that modeling analysis revealed that the potential climatic effect caused by the project were mainly limited to the local scale or near-surface layer. Undoubtedly, this result seemed to be positive with considerable significance. (5) As China’s largest reservoir, greenhouse emissions from the reservoir have been the concern of academic communities, stakeholders, and policymakers, particularly about its potential contribution to China’s road to carbon neutrality. The special issue collected recent advances and outlooks on field monitoring and analysis of CO2 and CH4 fluxes in the reservoir. We believed that this would be a research hot spot shortly. This is the fourth special issue in the Journal of Lake Sciences over the past decade. It is not the number of manuscripts that counts but the quality of the research. In the future, we will continue to focus on the Three Gorges Reservoir, and report on the state of the research on hydrology, ecology, and environment and watershed water security in the Yangtze River Basin in the Post-Three-Gorges-Project era. These efforts will better serve the Great Protection Strategy of the Yangtze River and ecological civilization in China.

The core root microbiome of Spartina alterniflora is predominated by sulfur-oxidizing and sulfate-reducing bacteria in Georgia salt marshes, USA

BackgroundSalt marshes are dominated by the smooth cordgrass Spartina alterniflora on the US Atlantic and Gulf of Mexico coastlines. Although soil microorganisms are well known to mediate important biogeochemical cycles in salt marshes, little is known about the role of root microbiomes in supporting the health and productivity of marsh plant hosts. Leveraging in situ gradients in aboveground plant biomass as a natural laboratory, we investigated the relationships between S. alterniflora primary productivity, sediment redox potential, and the physiological ecology of bulk sediment, rhizosphere, and root microbial communities at two Georgia barrier islands over two growing seasons.ResultsA marked decrease in prokaryotic alpha diversity with high abundance and increased phylogenetic dispersion was found in the S. alterniflora root microbiome. Significantly higher rates of enzymatic organic matter decomposition, as well as the relative abundances of putative sulfur (S)-oxidizing, sulfate-reducing, and nitrifying prokaryotes correlated with plant productivity. Moreover, these functional guilds were overrepresented in the S. alterniflora rhizosphere and root core microbiomes. Core microbiome bacteria from the Candidatus Thiodiazotropha genus, with the metabolic potential to couple S oxidation with C and N fixation, were shown to be highly abundant in the root and rhizosphere of S. alterniflora.ConclusionsThe S. alterniflora root microbiome is dominated by highly active and competitive species taking advantage of available carbon substrates in the oxidized root zone. Two microbially mediated mechanisms are proposed to stimulate S. alterniflora primary productivity: (i) enhanced microbial activity replenishes nutrients and terminal electron acceptors in higher biomass stands, and (ii) coupling of chemolithotrophic S oxidation with carbon (C) and nitrogen (N) fixation by root- and rhizosphere-associated prokaryotes detoxifies sulfide in the root zone while potentially transferring fixed C and N to the host plant.5gNBGD5xoDXmzcUFa4HG9gVideo

Unexpected Consequences of River Engineering on the Carbon Cycle

AbstractRivers around the world have been heavily engineered, and these man‐made changes are affecting important biogeochemical cycles. Rivers play a key role in the global carbon cycle, by mobilizing organic carbon from land and delivering it to the oceans. River engineering techniques, like levees that prevent flooding, change the way carbon is cycled through rivers, but it is difficult to identify and quantify these changes. Shen et al. (2021) were able to quantify changes in river organic carbon fluxes induced by bank stabilization in the Mississippi River. The authors compared the age distribution of organic carbon in modern river sediment and old river sediment deposited before the construction of extensive levee systems. They found that bank stabilization significantly reduces the amount of time organic carbon spends in the river system before being exported to the Gulf of Mexico. As a result, less organic carbon is oxidized to CO2 and more organic carbon is exported to the ocean, ultimately reducing atmospheric CO2. This study highlights an important effect of anthropogenic activity on river carbon fluxes that should be considered in global carbon cycle models.

Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline.

One of the major methods to identify microbial community composition, to unravel microbial population dynamics, and to explore microbial diversity in environmental samples is high-throughput DNA- or RNA-based 16S rRNA (gene) amplicon sequencing in combination with bioinformatics analyses. However, focusing on environmental samples from contrasting habitats, it was not systematically evaluated (i) which analysis methods provide results that reflect reality most accurately, (ii) how the interpretations of microbial community studies are biased by different analysis methods and (iii) if the most optimal analysis workflow can be implemented in an easy-to-use pipeline. Here, we compared the performance of 16S rRNA (gene) amplicon sequencing analysis tools (i.e., Mothur, QIIME1, QIIME2, and MEGAN) using three mock datasets with known microbial community composition that differed in sequencing quality, species number and abundance distribution (i.e., even or uneven), and phylogenetic diversity (i.e., closely related or well-separated amplicon sequences). Our results showed that QIIME2 outcompeted all other investigated tools in sequence recovery (>10 times fewer false positives), taxonomic assignments (>22% better F-score) and diversity estimates (>5% better assessment), suggesting that this approach is able to reflect the in situ microbial community most accurately. Further analysis of 24 environmental datasets obtained from four contrasting terrestrial and freshwater sites revealed dramatic differences in the resulting microbial community composition for all pipelines at genus level. For instance, at the investigated river water sites Sphaerotilus was only reported when using QIIME1 (8% abundance) and Agitococcus with QIIME1 or QIIME2 (2 or 3% abundance, respectively), but both genera remained undetected when analyzed with Mothur or MEGAN. Since these abundant taxa probably have implications for important biogeochemical cycles (e.g., nitrate and sulfate reduction) at these sites, their detection and semi-quantitative enumeration is crucial for valid interpretations. A high-performance computing conformant workflow was constructed to allow FAIR (Findable, Accessible, Interoperable, and Re-usable) 16S rRNA (gene) amplicon sequence analysis starting from raw sequence files, using the most optimal methods identified in our study. Our presented workflow should be considered for future studies, thereby facilitating the analysis of high-throughput 16S rRNA (gene) sequencing data substantially, while maximizing reliability and confidence in microbial community data analysis.

Microorganisms and Their Metabolic Capabilities in the Context of the Biogeochemical Nitrogen Cycle at Extreme Environments.

Extreme microorganisms (extremophile) are organisms that inhabit environments characterized by inhospitable parameters for most live beings (extreme temperatures and pH values, high or low ionic strength, pressure, or scarcity of nutrients). To grow optimally under these conditions, extremophiles have evolved molecular adaptations affecting their physiology, metabolism, cell signaling, etc. Due to their peculiarities in terms of physiology and metabolism, they have become good models for (i) understanding the limits of life on Earth, (ii) exploring the possible existence of extraterrestrial life (Astrobiology), or (iii) to look for potential applications in biotechnology. Recent research has revealed that extremophilic microbes play key roles in all biogeochemical cycles on Earth. Nitrogen cycle (N-cycle) is one of the most important biogeochemical cycles in nature; thanks to it, nitrogen is converted into multiple chemical forms, which circulate among atmospheric, terrestrial and aquatic ecosystems. This review summarizes recent knowledge on the role of extreme microorganisms in the N-cycle in extremophilic ecosystems, with special emphasis on members of the Archaea domain. Potential implications of these microbes in global warming and nitrogen balance, as well as their biotechnological applications are also discussed.

Benchmarking protocols for the metagenomic analysis of stream biofilm viromes.

Viruses drive microbial diversity, function and evolution and influence important biogeochemical cycles in aquatic ecosystems. Despite their relevance, we currently lack an understanding of their potential impacts on stream biofilm structure and function. This is surprising given the critical role of biofilms for stream ecosystem processes. Currently, the study of viruses in stream biofilms is hindered by the lack of an optimized protocol for their extraction, concentration and purification. Here, we evaluate a range of methods to separate viral particles from stream biofilms, and to concentrate and purify them prior to DNA extraction and metagenome sequencing. Based on epifluorescence microscopy counts of viral-like particles (VLP) and DNA yields, we optimize a protocol including treatment with tetrasodium pyrophosphate and ultra-sonication to disintegrate biofilms, tangential-flow filtration to extract and concentrate VLP, followed by ultracentrifugation in a sucrose density gradient to isolate VLP from the biofilm slurry. Viromes derived from biofilms sampled from three different streams were dominated by Siphoviridae, Myoviridae and Podoviridae and provide first insights into the viral diversity of stream biofilms. Our protocol optimization provides an important step towards a better understanding of the ecological role of viruses in stream biofilms.

Chemical and microbial diversity covary in fresh water to influence ecosystem functioning

Invisible to the naked eye lies a tremendous diversity of organic molecules and organisms that make major contributions to important biogeochemical cycles. However, how the diversity and composition of these two communities are interlinked remains poorly characterized in fresh waters, despite the potential for chemical and microbial diversity to promote one another. Here we exploited gradients in chemodiversity within a common microbial pool to test how chemical and biological diversity covary and characterized the implications for ecosystem functioning. We found that both chemodiversity and genes associated with organic matter decomposition increased as more plant litterfall accumulated in experimental lake sediments, consistent with scenarios of future environmental change. Chemical and microbial diversity were also positively correlated, with dissolved organic matter having stronger effects on microbes than vice versa. Under our experimental scenarios that increased sediment organic matter from 5 to 25% or darkened overlying waters by 2.5 times, the resulting increases in chemodiversity could increase greenhouse gas concentrations in lake sediments by an average of 1.5 to 2.7 times, when all of the other effects of litterfall and water color were considered. Our results open a major new avenue for research in aquatic ecosystems by exposing connections between chemical and microbial diversity and their implications for the global carbon cycle in greater detail than ever before.

Distinct Microbial Community of Phyllosphere Associated with Five Tropical Plants on Yongxing Island, South China Sea.

The surfaces of a leaf are unique and wide habitats for a microbial community. These microorganisms play a key role in plant growth and adaptation to adverse conditions, such as producing growth factors to promote plant growth and inhibiting pathogens to protect host plants. The composition of microbial communities very greatly amongst different plant species, yet there is little data on the composition of the microbiome of the host plants on the coral island in the South China Sea. In this study, we investigated the abundances and members of a major microbial community (fungi, bacteria, and diazotrophs) on the leaves of five dominant plant species (Ipomoea pes-caprae, Wedelia chinensis, Scaevola sericea, Cocos nucifera, and Sesuvium portulacastrum) on the island using real-time quantitative polymerase chain reaction (PCR) and high-throughput amplicon sequencing. Quantitative PCR results showed that fungi and bacteria were ubiquitous and variable among different host plants. Scaevola sericea showed the lowest absolute abundance and highest diversity of fungi and bacteria, while Cocos nucifera had the lowest abundance and the highest diversity of diazotrophs compare to the other four plants. There was a small proportion of shared microorganisms among the five different plants, while unique fungi, bacteria and diazotrophs were significantly enriched for different host plant species in this study (p < 0.05). Some of the most abundant organisms found in the communities of these different host plants are involved in important biogeochemical cycles that can benefit their host, including carbon and nitrogen cycles.

Key Metabolic Pathways of Sulfur Metabolism and Bacterial Diversity under Elevated CO2 and Temperature in Lowland Rice: A Metagenomic Approach

Sulfur (S) metabolism is an important biogeochemical cycles in lowland rice. However, S biogeochemistry in rice soil is underestimated due to low standing pools of sulfate and unknown taxa of sulfur-reducing microorganisms. A whole-genome metagenomic study considering KEGG pathways and prevalence of enzymatic assay could provide an insight of dominating pathways of S-metabolism which are important in the context of S nutrition to plant and of mitigating GHGs emission in relation to climate change feedback. In this study, soil bacterial diversity and S-metabolism pathways were studied under ambient CO2 (a-CO2) and elevated CO2 + temperature (e-CO2T) in lowland rice. The assimilatory pathway was the dominant irrespective of atmospheric CO2 concentrations indicated higher influence of ecology than atmospheric condition. The phylum Proteobacteria and Firmicutes were dominant and showed an abundance of 54 and 12%, under a-CO2 and e-CO2T, respectively. Desulfovibrio was the most dominant genus. Desulfatibacillum, Desulfotomaculum, Desulfococcus, and Desulfitobacterium also showed higher abundance reads under e-CO2T. As a whole, total bacterial diversities were more under a-CO2, whereas, the activities of dominant bacteria were higher under e-CO2T. Shannon–Weaver and Simpson indices were higher under e-CO2T than a-CO2. The targeted gene-based quantification of bacteria responsible for S-metabolism is the future need.

Evidence for microbial iron reduction in the methanic sediments of the oligotrophic southeastern Mediterranean continental shelf

Abstract. Dissimilatory iron reduction is probably one of the oldest types of metabolisms that still participates in important biogeochemical cycles, such as those of carbon and sulfur. It is one of the more energetically favorable anaerobic microbial respiration processes and is usually coupled to the oxidation of organic matter. Traditionally this process is thought to be limited to the shallow part of the sedimentary column in most aquatic systems. However, iron reduction has also been observed in the methanic zone of many marine and freshwater sediments, well below its expected zone and occasionally accompanied by decreases in methane, suggesting a link between the iron and the methane cycles. Nevertheless, the mechanistic nature of this link (competition, redox or other) has yet to be established and has not been studied in oligotrophic shallow marine sediments. In this study we present combined geochemical and molecular evidences for microbial iron reduction in the methanic zone of the oligotrophic southeastern (SE) Mediterranean continental shelf. Geochemical porewater profiles indicate iron reduction in two zones, the uppermost part of the sediment, and the deeper zone, in the layer of high methane concentration. Results from a slurry incubation experiment indicate that the deep methanic iron reduction is microbially mediated. The sedimentary profiles of microbial abundance and quantitative PCR (qPCR) of the mcrA gene, together with Spearman correlation between the microbial data and Fe(II) concentrations in the porewater, suggest types of potential microorganisms that may be involved in the iron reduction via several potential pathways: H2 or organic matter oxidation, an active sulfur cycle, or iron-driven anaerobic oxidation of methane. We suggest that significant upward migration of methane in the sedimentary column and its oxidation by sulfate may fuel the microbial activity in the sulfate methane transition zone (SMTZ). The biomass created by this microbial activity can be used by the iron reducers below, in the methanic zone of the sediments of the SE Mediterranean.

Reversing nitrogen fixation

The nitrogen cycle is one of the most important biogeochemical cycles on Earth because nitrogen is an essential nutrient for all life forms. To supplement natural nitrogen fixation, farmers add large amounts of nitrogen-containing fertilizer to their soils such that nitrogen never becomes a limiting nutrient for plant growth. However, of the nitrogen added to fields — most of which is in the form of NH3 and NO3− — only 30–50% is taken up by plants, while the remainder is metabolized by soil microorganisms in processes with detrimental environmental impacts. The first of these processes, that is, nitrification, refers to the biological oxidation of NH3 to NO2− and NO3−, which have low retention in soil and pollute waterways, leading to downstream eutrophication and ultimately ‘dead zones’ (low oxygen zones) in coastal waters, for example, the Gulf of Mexico. In a second process, namely, denitrification, NO3− and NO2− undergo stepwise reduction to N2O and N2. Substantial amounts of the N2O produced in this process escape into the atmosphere, contributing to climate change and ozone destruction. Recent results suggest that nitrification also affords N2O. This Review describes the enzymes involved in NH3 oxidation and N2O production and degradation in the nitrogen cycle. We pay particular attention to the active site structures, the associated coordination chemistry that enables the chemical transformations and the reaction mechanisms. Nitrification and denitrification are responsible for the processing of ammonia fertilizer, ultimately leading to the generation of environmental pollutants that accumulate in waterways and the atmosphere. This Review describes the enzymes involved in these processes, which fascinate with their unusual active sites and the surprising reactions that they catalyse.

Submarine groundwater discharge and solute transport under a transgressive barrier island

Many recent investigations of groundwater dynamics in beaches employed groundwater models that assumed isotropic, numerically-convenient hydrogeological conditions. Real beaches exhibit local variability with respect to stratigraphy, sediment grain size and associated topographic profile, so that groundwater flow may diverge significantly from idealized models. We used a combination of hydrogeologic field methods and a variable-density, saturated-unsaturated, transient groundwater flow model to investigate SGD and solute transport under Cabretta Beach, a small transgressive barrier island seaward of Sapelo Island, Georgia. We found that the inclusion of real beach heterogeneity drove important deviations from predictions based on theoretical beaches. Cabretta Beach sustained a stronger upper saline plume than predicted due to the presence of a buried silty mud layer beneath the surface. Infiltration of seawater was greater for neap tides than for spring tides due to variations in beach slope. The strength of the upper saline plume was greatest during spring tides, contrary to recent model predictions. The position and width of the upper saline plume was highly dynamic through the lunar cycle. Our results suggest that field measurements of salinity gradients may be useful for estimating rates of tidally and density driven recirculation through the beach. Finally, our results indicate that several important biogeochemical cycles recently studied at Cabretta Beach were heavily influenced by groundwater flow and associated solute transport.

Surface ocean-lower atmosphere study: Scientific synthesis and contribution to Earth system science

The domain of the surface ocean and lower atmosphere is a complex, highly dynamic component of the Earth system. Better understanding of the physics and biogeochemistry of the air–sea interface and the processes that control the exchange of mass and energy across that boundary define the scope of the Surface Ocean-Lower Atmosphere Study (SOLAS) project. The scientific questions driving SOLAS research, as laid out in the SOLAS Science Plan and Implementation Strategy for the period 2004–2014, are highly challenging, inherently multidisciplinary and broad. During that decade, SOLAS has significantly advanced our knowledge. Discoveries related to the physics of exchange, global trace gas budgets and atmospheric chemistry, the CLAW hypothesis (named after its authors, Charlson, Lovelock, Andreae and Warren), and the influence of nutrients and ocean productivity on important biogeochemical cycles, have substantially changed our views of how the Earth system works and revealed knowledge gaps in our understanding. As such SOLAS has been instrumental in contributing to the International Geosphere–Biosphere Programme (IGBP) mission of identification and assessment of risks posed to society and ecosystems by major changes in the Earth’s biological, chemical and physical cycles and processes during the Anthropocene epoch. SOLAS is a bottom-up organization, whose scientific priorities evolve in response to scientific developments and community needs, which has led to the launch of a new 10-year phase. SOLAS (2015–2025) will focus on five core science themes that will provide a scientific basis for understanding and projecting future environmental change and for developing tools to inform societal decision-making.

The role of phytoplankton diversity in the emergent oceanic stoichiometry

Marine phytoplankton are a taxonomically and functionally diverse group of organisms that are key players in the most important biogeochemical cycles. Phytoplankton taxa show different resource utilization strategies (e.g. nutrient-uptake rates and cellular allocation) and traits. Therefore, acknowledging this diversity is crucial to understanding how elemental cycles operate, including the origin and dynamics of elemental ratios. In this paper, we focus on trait-based models as tools to study the role of phytoplankton diversity in the stoichiometric phenomenology observed in the laboratory and in the open ocean. We offer a compilation of known empirical results on stoichiometry and summarize how trait-based approaches have attempted to replicate these results. By contrasting the different ecological and evolutionary approaches available in the literature, we explore the strengths and limitations of the existing models. We thus try to identify existing gaps and challenges, and point to potential new directions that can be explored to fill these gaps. We aim to highlight the potential of including diversity explicitly in our modeling approaches, which can help us gain important knowledge about changes in local and global stoichiometric patterns.