Biogeochemistry: its origins and development

The history of how aspects of biology, geology and chemistry came together over the past three centuries to form a separate discipline known as biogeochemistry is described under four major headings: metabolic aspects, geochemical aspects, biogeochemical cycles, and the origin of life. A brief chronology of major conceptual advances is also presented.     

Peat and water chemistry at Big Run Bog,a peatland in the Appalachian mountains of West Virginia,USA

At Big Run Bog, aSphagnum-dominated peatland in the unglaciated Appalachian Plateau of West Virginia, significant spatial variation in the physical and chemical properties of the peat and in surface and subsurface (30 cm deep) water chemistry was characterized. The top 40 cm of organic peat at Big Run Bog had average values for bulk density of 0.09 g · cm^–3, organic matter concentration of 77%, and volumetric water content of 88%. Changes in physical and chemical properties within the peat column as a function of depth contributed to different patterns of seasonal variation in the chemistry of surface and subsurface waters. Seasonal variation in water chemistry was related to temporal changes in plant uptake, organic matter decomposition and element mineralization, and to varying redox conditions associated with fluctuating water table levels. On the average, total Ca, Mg, and N concentrations in Big Run Bog peat were 33, 15, and 1050 mol · g^–1, respectively; exchangeable Ca and Mg concentrations were 45 and 14 eq · g^–1 , respectively. Surface water pH averaged 4.0 and Ca⁺⁺ concentrations were less than 50 eq · L^–1 . These chemical variables have all been used to distinguish bogs from fens. Physiographically, Big Run Bog is a minerotrophic fen because it receives inputs of water from the surrounding forested upland areas of its watershed. However, chemically, Big Run Bog is more similar to true ombrotrophic bogs than to minerotrophic fens.     

The evolution of saline lake waters: gradual and rapid biogeochemical pathways in the Basotu Lake District,Tanzania

The biogeochemical evolution of solutes markedly alters the chemistry in the closed-basin maar lakes that comprise the Basotu Lake District (Tanzania, East Africa). Examination of 11 (out of 13) lakes in the Basotu Lake District identified two distinct evolutionary pathways: a gradual path and a rapid path. During the course of biogeochemical evolution these waters follow either the gradual path alone or a combination of the gradual and rapid paths. Solute evolution along the gradual path is determined by all of the biogeochemical processes that for these waters appear to be tightly coupled to evaporative concentration (e.g. mineral precipitation, sorption and ion exchange, C0₂ degassing, and sulfate reduction). Rapid evolution occurs when mixing events suddenly permit H₂S to be lost to the atmosphere. The chemistry of waters undergoing rapid evolution is changed abruptly because loss of every equivalent of sulfide produces an equivalent permanent alkalinity.The Basotu Lake District in north central Tanzania is comprised of 13 maar lakes. They range in surface water conductivity from 592 to 24 000 µ S cm ^–1 (at 20°). Within these lake basins only a few of the variety of geo- and biogeochemical processes known to occur in lakes of this type are actually responsible for the gain and/or loss of individual solutes. For example, potassium appears to be taken up in the formation of illite. Calcium is precipitated as calcite. Magnesium interacts with alumino-silicate precursors to form a variety of clay minerals that contain magnesium (e.g. stevensite). This process is also known as reverse weathering. Sulfate is reduced to sulfide and subsequently lost as H₂S and/or metal sulfides. Alkalinity is lost owing to calcite precipitation and as a consequence of reverse weathering. Alkalinity is gained in the form of extra permanent alkalinity when sulfide is lost from these waters (via metal sulfide precipitation or gaseous emission to the atmosphere). Rapid (punctuated) evolution can occur in any lake containing anoxic waters providing that mixing events take place which cause H₂S to be lost to the atmosphere.Peter Kilham died on March 20, 1989, in Kisumu, Kenya, while working as part of a research team on Lake Victoria.     

Dissolved and suspended mercury. species in the Wabigoon River (Ontario,Canada): seasonal and regional variations

Seasonal and regional variations in the speciation, sediment-water partitioning, and dynamics of mercury (Hg) were studied at selected sites along the Hg-polluted Wabigoon River, and at unpolluted headwater and tributary sites, during April–September, 1979. ‘Dissolved’ and ‘particulate’ forms of Hg in the water were separated by continuous-flow centrifugation in the field. The Hg and other pollutants such as wood chips and salt had been discharged from a chlor-alkali plant and paper mill at Dryden, Ontario. Concentrations and loadings of particulate methyl mercury (CH₃Hg⁺) and total particulate Hg (and loadings of total ‘dissolved’ Hg) were greatest during the spring flood (April-May) owing to accelerated resuspension and transport of sediments. Concentrations of ‘dissolved’ CH₃Hg⁺, however, were highest in the summer (July–September), probably reflecting stimulation of microbial methylating activity by elevated temperatures, together with factors such as reduced levels of metal-scavenging particulates and minimal dilution by runoff. Total dissolved Hg concentrations were relatively high in September at polluted sites only, possibly because of desorption from sediments due to elevated concentrations of Cl⁻ ions. Loadings of dissolved CH₃Hg⁺ tended to be high in the summer but were generally depressed (suggesting sorption by suspended particles) during the major spring-flood episode in May. During July–August dissolved CH₃Hg⁺ was a function of total dissolved Hg, suggesting rapid biomethylation of desorbed inorganic Hg; but in general dissolved and suspended CH₃Hg⁺ levels depended on environmental variables and were unrelated to total Hg concentrations. In the summer only, total dissolved Hg was a function of dissolved Cl⁻. Hg species in particulates were associated with sulfides, hydrated Fe and Mn oxides, organic matter (notably high molecular weight humic and humic-Fe components), and selenium (Se); but CH₃Hg⁺ and total Hg differed in their specific preferences for binding agents, implying that binding sites discriminate between CH₃Hg⁺ and Hg²⁺ ions. CH₃Hg⁺ was associated with sulfide and (in the spring only) with Fe oxides, whereas total Hg was associated with organic matter and Se and with DTPA- and NaOH-extractable Fe in the spring but with Mn oxide and NaOH-extractable organics in the summer. Sulfides were most abundant in May, indicating that they were eroded from bottom sediments, but Fe and Mn oxides were most abundant in the summer, probably owing to activities of filamentous iron bacteria and other micro-organisms. Particulate Hg was 98–100% nonextractable by mild solvents such as Ca acetate, CaCl₂, dilute acetic acid, and (at polluted sites only) DTPA solutions, suggesting that the particulate Hg mobilized in the spring may not be readily available to organisms; association with Se and high molecular weight humic matter also supports this hypothesis. Hg probably becomes more bio-available in the summer, as suggested by the upsurge in dissolved CH₃Hg⁺ and total dissolved Hg levels, and by increases in the solubility of particulate Hg in acetic acid, DTPA, H₂O₂, and NaOH solutions, as well as an increase in the relative importance of lower molecular weight fractions of NaOH-extractable Hg (in September). Regional variations in Hg speciation and partitioning reflected a gradient in sediment composition from wood chips near Dryden to silt-clay mud further downstream. Hg in silt-clay mud relatively far (> 35 km) downstream from the source of pollution or in unpolluted areas appeared to be more readily solubilized by Cl⁻ ions or chelators such as DTPA, more readily methylated (as indicated by downstream increases in dissolved CH₃Hg⁺ levels and CH₃Hg⁺/total Hg ratios), and was to a greater degree organically bound (H₂O₂-extractable), and thus was probably more bio-available, than Hg in wood-chip deposits. Possible explanations include weaker binding of Hg by the mud, the more finely divided state of the mud, and improved microbial growth at lower concentrations of toxic pollutants. Owing to enrichment in sulfides and Fe oxides, resuspended wood-chip sediments were especially efficient scavengers of CH₃Hg⁺. The results indicate that in any pollution abatement plan aimed at lowering the Hg levels in the biota of lakes fed by the Wabigoon River, immobilization, removal, or detoxification of dissolved as well as particulate forms of Hg in the river would probably have to be considered. Possibly, Hg species could be ‘scrubbed’ from the river water by increasing the suspended load and by sedimentation and treatment with Hg-binding agents in special receiving basins.     

Tidal downwelling and implications for the carbon biogeochemistry of cold‐water corals in relation to future ocean acidification and warming

Cold‐water coral (CWC) reefs are recognized as ecologically and biologically significant areas that generate habitats and diversity. The interaction between hydrodynamics and CWCs has been well studied at the Mingulay Reef Complex, a relatively shallow area of reefs found on the continental shelf off Scotland, UK. Within ‘Mingulay Area 01’ a rapid tidal downwelling of surface waters, brought about as an internal wave, is known to supply warmer, phytoplankton‐rich waters to corals growing on the northern flank of an east‐west trending seabed ridge. This study shows that this tidal downwelling also causes short‐term perturbations in the inorganic carbon (C_T) and nutrient dynamics through the water column and immediately above the reef. Over a 14 h period, corresponding to one semi‐diurnal tidal cycle, seawater pH overlying the reef varied by ca. 0.1 pH unit, while pCO₂ shifted by >60 μatm, a shift equivalent to a ca. 25 year jump into the future, with respect to atmospheric pCO₂. During the summer stratified period, these downwelling events result in the reef being washed over with surface water that has higher pH, is warmer, nutrient depleted, but rich in phytoplankton‐derived particles compared to the deeper waters in which the corals sit. Empirical observations, together with outputs from the European Regional Shelf Sea Ecosystem Model, demonstrate that the variability that the CWC reefs experience changes through the seasons and into the future. Hence, as ocean acidification and warming increase into the future, the downwelling event specific to this site could provide short‐term amelioration of corrosive conditions at certain times of the year; however, it could additionally result in enhanced detrimental impacts of warming on CWCs. Natural variability in the C_T and nutrient conditions, as well as local hydrodynamic regimes, must be accounted for in any future predictions concerning the responses of marine ecosystems to climate change.     

Further reading in geomicrobiology

In the wetland rhizosphere, high densities of lithotrophic Fe(II)-oxidizing bacteria (FeOB) and a favorable environment (i.e., high Fe(II) availability and microaerobic conditions) suggest that these organisms are actively contributing to the formation of Fe plaque on plant roots. We manipulated the presence/absence of an Fe(II)-oxidizing bacterium (Sideroxydans paludicola, strain BrT) in axenic hydroponic microcosms containing the roots of intact Juncus effusus (soft rush) plants to determine if FeOB affected total rates of rhizosphere Fe(II) oxidation and Fe plaque accumulation. Our experimental data highlight the importance of both FeOB and plants in influencing short-term rates of rhizosphere Fe oxidation. Over time scales ca. 1 wk, the FeOB increased Fe(II) oxidation rates by 1.3 to 1.7 times relative to FeOB-free microcosms. Across multiple experimental trials, Fe(II) oxidation rates were significantly correlated with root biomass, reflecting the importance of radial O ₂ loss in supporting rhizosphere Fe(II) oxidation. Rates of root Fe(III) plaque accumulation (time scales: 3 to 6 wk) were ～ 70 to 83% lower than expected based on the short-term Fe(II) oxidation rates and were unaffected by the presence/absence of FeOB. Decreasing rates of Fe(II) oxidation and Fe(III) plaque accumulation with increasing time scales indicate changes in rates of Fe(II) diffusion and radial O ₂ loss, shifts in the location of Fe oxide accumulation, or temporal changes in the microbial community within the microcosms. The microcosms used herein replicated many of the environmental characteristics of wetland systems and allowed us to demonstrate that FeOB can stimulate rates of Fe(II) oxidation in the wetland rhizosphere, a finding that has implications for the biogeochemical cycling of carbon, metals, and nutrients in wetland ecosystems.     

Energy,ecology and the distribution of microbial life

Mechanisms that govern the coexistence of multiple biological species have been studied intensively by ecologists since the turn of the nineteenth century. Microbial ecologists in the meantime have faced many fundamental challenges, such as the lack of an ecologically coherent species definition, lack of adequate methods for evaluating population sizes and community composition in nature, and enormous taxonomic and functional diversity. The accessibility of powerful, culture-independent molecular microbiology methods offers an opportunity to close the gap between microbial science and the main stream of ecological theory, with the promise of new insights and tools needed to meet the grand challenges humans face as planetary engineers and galactic explorers. We focus specifically on resources related to energy metabolism because of their direct links to elemental cycling in the Earth''s history, engineering applications and astrobiology. To what extent does the availability of energy resources structure microbial communities in nature? Our recent work on sulfur- and iron-oxidizing autotrophs suggests that apparently subtle variations in the concentration ratios of external electron donors and acceptors select for different microbial populations. We show that quantitative knowledge of microbial energy niches (population-specific patterns of energy resource use) can be used to predict variations in the abundance of specific taxa in microbial communities. Furthermore, we propose that resource ratio theory applied to micro-organisms will provide a useful framework for identifying how environmental communities are organized in space and time.     

Grazers: biocatalysts of terrestrial silica cycling

Silica is well known for its role as inducible defence mechanism countering herbivore attack, mainly through precipitation of opaline, biogenic silica (BSi) bodies (phytoliths) in plant epidermal tissues. Even though grazing strongly interacts with other element cycles, its impact on terrestrial silica cycling has never been thoroughly considered. Here, BSi content of ingested grass, hay and faeces of large herbivores was quantified by performing multiple chemical extraction procedures for BSi, allowing the assessment of chemical reactivity. Dissolution experiments with grass and faeces were carried out to measure direct availability of BSi for dissolution. Average BSi and readily soluble silica numbers were higher in faeces as compared with grass or hay, and differences between herbivores could be related to distinct digestive strategies. Reactivity and dissolvability of BSi increases after digestion, mainly due to degradation of organic matrices, resulting in higher silica turnover rates and mobilization potential from terrestrial to aquatic ecosystems in non-grazed versus grazed pasture systems (2 versus 20 kg Si ha⁻¹ y⁻¹). Our results suggest a crucial yet currently unexplored role of herbivores in determining silica export from land to ocean, where its availability is linked to eutrophication events and carbon sequestration through C–Si diatom interactions.     

稳定碳同位素在滨海湿地碳生物地球化学循环中的应用

碳作为滨海湿地中重要的生命元素,其生物地球化学循环过程是滨海湿地研究的核心内容之一.稳定同位素技术越来越多地被应用到滨海湿地碳生物地球化学循环过程的研究中,提高了其研究水平,并推动了其研究的进程.本文从有机物质生产、土壤有机质来源、食物链传递、温室气体排放以及可溶性有机碳输出5个方面,综述了滨海湿地碳生物地球化学循环过程的稳定同位素研究进展.通过植物及土壤δ13C值的测定进行有机质的生产机理研究及外源追溯,通过对比各生物种群的δ13C值分析碳在生态系统中的流动过程,通过湿地排放温室气体及可溶性有机碳δ13C值的测定揭示影响碳输出的环境因子.最后,文章总结了当前研究中存在的问题,并对其研究前景进行了展望.