Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor

Microbial methanogenesis in subseafloor sediments is a key process in the carbon cycle on the Earth. However, the cultivation-dependent evidences have been poorly demonstrated. Here we report the cultivation of a methanogenic microbial consortium from subseafloor sediments using a continuous-flow-type bioreactor with polyurethane sponges as microbial habitats, called down-flow hanging sponge (DHS) reactor. We anaerobically incubated methane-rich core sediments collected from off Shimokita Peninsula, Japan, for 826 days in the reactor at 10 °C. Synthetic seawater supplemented with glucose, yeast extract, acetate and propionate as potential energy sources was provided into the reactor. After 289 days of operation, microbiological methane production became evident. Fluorescence in situ hybridization analysis revealed the presence of metabolically active microbial cells with various morphologies in the reactor. DNA- and RNA-based phylogenetic analyses targeting 16S rRNA indicated the successful growth of phylogenetically diverse microbial components during cultivation in the reactor. Most of the phylotypes in the reactor, once it made methane, were more closely related to culture sequences than to the subsurface environmental sequence. Potentially methanogenic phylotypes related to the genera Methanobacterium, Methanococcoides and Methanosarcina were predominantly detected concomitantly with methane production, while uncultured archaeal phylotypes were also detected. Using the methanogenic community enrichment as subsequent inocula, traditional batch-type cultivations led to the successful isolation of several anaerobic microbes including those methanogens. Our results substantiate that the DHS bioreactor is a useful system for the enrichment of numerous fastidious microbes from subseafloor sediments and will enable the physiological and ecological characterization of pure cultures of previously uncultivated subseafloor microbial life.     

Effects of temperature and sediment properties on benthic CO2 production in an oligotrophic boreal lake

1. Temperature and many other physical and chemical factors affecting CO₂ production in lake sediments vary significantly both seasonally and spatially. The effects of temperature and sediment properties on benthic CO₂ production were studied in in situ and in vitro experiments in the boreal oligotrophic Lake Pääjärvi, southern Finland. 2. In in situ experiments, temperature of the water overlying the shallow littoral sediment varied seasonally between 0.5 and 15.7 °C, but in deep water (≥20 m) the range was only 1.1–6.6 °C. The same exponential model (r² = 0.70) described the temperature dependence at 1.2, 10 and 20 m depths. At 2.5 and 5 m depths, however, the slopes of the two regression models (r² = 0.94) were identical but the intercept values were different. Sediment properties (wet, dry, mineral and organic mass) varied seasonally and with depth, but they did not explain a significantly larger proportion of variation in the CO₂ output rate than temperature. 3. In in vitro experiments, there was a clear and uniform exponential dependence of CO₂ production on temperature, with a 2.7‐fold increase per 10 °C temperature rise. The temperature response (slope of regression) was always the same, but the basic value of CO₂ production (intercept) varied, indicating that other factors also contributed to the benthic CO₂ output rate. 4. The annual CO₂ production of the sediment in Lake Pääjärvi averaged 62 g CO₂ m^?2, the shallow littoral at 0–3 m depth releasing 114 g CO₂ m^?2 and deep profundal (>15 m) 30 g CO₂ m^?2. On the whole lake basis, the shallow littoral at 0–3 m depth accounted for 53% and the sediment area in contact with the summer epilimnion (down to a depth c. 10 m) 75% of the estimated total annual CO₂ output of the lake sediment, respectively. Of the annual production, 83% was released during the spring and summer. 5. Using the temperature‐CO₂ production equations and climate change scenarios we estimated that climatic warming might increase littoral benthic CO₂ production in summer by nearly 30% from the period 1961–90 to the period 2071–2100.     

Errors in the determination of low levels of nitrate in lake sediments

Abstract

Error sources associated with the spectrophotometric determination of low levels (e.g. <2 μg g^?1) of nitrate in sediments have been examined and problems identified included incomplete nitrate recovery (attributable in part to anion resorption) and light scattering by colloidal (<0.45 μm) matter in extract solutions (minimised by using uncoloured extract in the reference beam). Optimum retrieval (>90%) of nitrate from the marine lake sediments studied was achieved with 15 min mixing with 0.1 M NH₄CI, using a sediment to extractant ratio of 1:30. The nitrate in the extracts was determined by reducing it to nitrite (using Cd powder), with subsequent colour development based on the addition of sulfanilic acid and N-1-naphthyl-ethylenediamine dihydrochloride. The reduction step was sensitive to the experimental conditions used, but was near quantitative using 0.1 M NH₄CI extracts. (Much lower transformation levels were observed when the nitrate solutions contained KCI or CaSO₄, or when Zn powder was used as the reductant). All the sediments tested sorbed nitrate ion from solution (some very avidly) and this sorbed ion was not readily retrieved by back extraction into NH₄CI solutions.     

Spatial distribution of subfossil Chironomidae in surface sediments of a large, shallow and hypertrophic lake (Taihu, SE China)

Spatial heterogeneity of benthic communities has clear implications for estimating lake production, biodiversity as well as identifying representative sites for palaeolimnological studies. This study investigates chironomid variability and the controlling factors (i.e., environmental and spatial variables) in surface sediments from Taihu Lake (2,338 km²), a hypertrophic lake in the Yangtze delta in eastern China. The spatial distribution of chironomids shows distinct heterogeneity. Microchironomus tabarui-type and Tanypus dominate the midge communities around the estuaries, while Cricotopus sylvestris-type and Polypedilum nubifer-type are the predominant taxa in the East Bays and the East Taihu Lake. Redundancy analysis was used for exploring the relationships between chironomid variability and environmental and spatial stressors. Four variables were identified as significant factors that influence chironomid community structures. The high nutrient concentrations around the estuarial areas favor the development of nutrient-tolerant taxa. Water depth-related oxygen depletion in the open lake during algae blooms prohibits the survival of many organisms, except for a few hypoxic-resistant species. High transparency in the East Bays and the East Taihu Lake indirectly creates a favorite microhabitat for macrophyte-associated chironomid species through aquatic plants. Space per se is a significant forcing factor for organism community and distribution at scales of >1,000 km². It might be important to consider spatial variables more explicitly in future studies of chironomids in large lakes where multiple stressors make the interactions within the ecosystem more complicated. This study aims to illustrate the ecological characteristics of specific chironomid taxa related to a “microecosystem” which is contributed by the multiple environmental gradients within a large lake, and to provide empirical support for interpretation of palaeochironomid data.     

Determination of nitrite in lake sediments

Abstract

An evaluation of nitrite determination in marine lake sediments has shown that spectrophotometric measurements can be in error due to light scattering by colloidal (<0.2 μm) matter in extract solutions and incomplete nitrite recovery. The scatter error can be minimised by using uncoloured extract in the reference beam but precision at low levels remains poor (RSD 25 to 100%). Recovery tests on ‘spiked’ sediment indicated that optimum retrieval (～85%) occurred with 30 minute mixing with 0.2 M NH₄Cl, using a sediment to extractant ratio of 1:30. To counter this variable, calibration based on standard addition to sample suspensions is recommended. Modified procedure proposed is suitable for measuring up to 10 μg g^?1 of nitrite N; the lake sediments tested contained <100 ng g^?1     

Oxygen stress and reduced growth of Lobelia dortmanna in sandy lake sediments subject to organic enrichment

1. Lobelia dortmanna is a common representative of the small isoetid plants dominating the vegetation in nutrient‐poor lakes in Europe and North America. Because of large permeable root surfaces and continuous air lacunae Lobelia exchanges the majority of O₂ and CO₂ during photosynthesis across the roots. This leads to profound diel pulses of O₂ and CO₂ in sandy sediments with low microbial O₂ consumption rates. The ready radial root loss of O₂ may, however, make Lobelia very susceptible to more reducing sediments. Therefore, we grew Lobelia for 6 months on natural and organically enriched sandy sediments to test how: (i) root oxygenation influenced degradation of organic matter and depth profiles of N and C; (ii) Lobelia and microbial O₂ consumption rates influenced pool size and depth penetration of O₂ in the sediments; and (iii) sediment enrichment influenced growth and mineral nutrition of Lobelia. 2. Naturally low‐organic sediments (0.32% DW) accumulated organic C and N during the experiment as a result of growth of Lobelia and surface micro‐algae. In contrast, surface layers of enriched sediments (0.58, 0.87 and 2.46% DW) lost organic C and N because of enhanced mineralisation rates because of oxygen availability. In deeper layers of enriched sediments no significant differences in organic C and N pools were found between plant‐covered and plant‐free sediments probably because faster organic degradation because of root oxygenation was balanced by release of organic matter from the plants and because short roots with dense Fe‐Mn coatings in the most enriched sediments constrained O₂ release. 3. Depth‐integrated O₂ pools were much higher in light than darkness, higher in plant‐covered than plant‐free sediments and higher in sandy than in organically enriched sediments. All sediments had a primary O₂ maximum 1–2 mm below the sediment surface in light because of photosynthesis of micro‐algae. Plant‐covered sediments of low organic content (0.32 and 0.58% DW) also had a secondary deep maximum (2–4 cm) because of higher O₂ release from Lobelia roots than microbial O₂ consumption. Nitrification occurred here resulting in depletion of NH and accumulation of NO. In low organic sediments, oxygen pools increased with higher plant biomass both in light and darkness. The deep O₂ and NO₃ maxima disappeared in high organic sediments of greater O₂ consumption rates and smaller O₂ release rates. 4. Lobelia was stressed by increasing O₂ consumption rate of the sediments. Plant weight and leaf number declined twofold and maximum root length declined fourfold suggesting severe problems maintaining sufficient axial O₂ transport to the root tips because of rapid radial O₂ loss. Despite markedly higher nutrient concentrations in the enriched sediments, leaf‐N declined twofold and leaf‐P declined fourfold to growth‐limiting levels. These responses can be explained by constrains on mycorrhisal activity, root metabolism and vascular transport because of O₂ depletion. Management efforts to stop the decline and ensure the recovery of the isoetid vegetation should therefore focus on improving water quality as well as sediment suitability for growth.     

Importance of sediments in understanding nutrient cyclings in lakes

Inorganic and organic nutrients are continuously transported to lake bottoms by sedimentation. By various biological, physical, chemical and mechanical processes quantities of certain nutrients can be brought back to the free water again. This cycling between the sediments and water may occur according to various schemes dependent on lake type and bottom conditions. Lake morphology, temperature regimes, trophic level and sediment type can all strongly influence the size of nutrient pools and rates of turnover.The various activities of bacteria, benthic algae, macrophytes, benthic invertebrates and fish, in conjunction with influences of temperature, pH-values, Eh-values, water content, organic matter and elemental sediment composition, lead to the extremely complex nature of nutrient cycling. Three essential components of aquatic ecosystems are discussed, namely carbon, nitrogen and phosphorus.The objective of this paper is to illustrate in condensed form the heterogeneous nature of nutrient cycling processes. In addition, the importance of sediments in understanding nutrient cycling is discussed from a water management perspective.     

Dynamic Light Regulation of Photosynthesis (A Review)

Regulatory reactions providing the photosynthetic apparatus with the ability to respond to variations of irradiance by changes in activities of the light and the dark stages of photosynthesis within a time range of seconds and minutes are considered in the review. At the light stage, such reactions are related to the changes in both distribution of light energy between two photosystems and probability of nonphotochemical dissipation of absorbed quanta in PSI and PSII. These regulatory reactions operate in a negative feedback mode, thus avoiding overreduction of electron transport chain and minimizing the probability of generation of reactive oxygen species. The crucial role in preventing the generation of reactive oxygen species belongs to dynamic regulation of electron transport activity despite the presence of complex system of their detoxification in chloroplasts. In dark reactions of Calvin cycle, the regulatory responses involve a positive feedback principle being related to redox regulation of activities of several enzymes, which is sensitive to the reduction status of PSI acceptor side. The complex of regulatory reactions based on negative and positive feedback principles provides prolonged functioning of a chloroplast and high stability of photosynthetic activity under various light conditions.     

A large carbon pool and small sink in boreal Holocene lake sediments

Model‐based estimates suggest that lake sediments may be a significant, long‐term sink for organic carbon (C) at regional to global scales. These models have used various approaches to predict sediment storage at broad scales from very limited data sets. Here, we report a large‐scale direct assessment of the standing stock and sedimentation rate of C for a representative set of lakes in Finland. The 122 lakes were selected from the statistically selected Nordic Lake Survey database, they cover the entire country and the water quality represents the average lake water quality in Finland. Unlike all prior estimates, these data use sediment cores that comprise the entire sediment record. The data show that within Finland, aquatic ecosystems contain the second largest areal C stocks (19 kg C m^?2) after peatlands (72 kg C m^?2), and exceed by significant amounts stocks in the forest soil (uppermost 75cm; 7.2 kg C m^?2) and woody biomass (3.4 kg C m^?2). Kauppi et al. (1997). The Finnish estimate extrapolated over the boreal region gives a total C pool in lakes 19–27 Pg C, significantly lower than the previous model‐based estimates.     

微生物固碳的电子供给策略研究进展北大核心CSCD

随着生物化工技术的不断发展成熟,通过改造微生物已可以实现二氧化碳、甲烷等温室气体的固定、转化和利用,而电子传递及能量供给对微生物固碳效率起着决定性的作用。本文首先分析了好氧性嗜甲烷菌、化能自养微生物等天然微生物细胞内外的直接、间接电子传递系统。在此基础上,围绕微生物固碳细胞工厂的构建,进一步介绍了基于光能、电能的人工电子供给策略及其对固碳过程中代谢通量、合成路径和供能效率的影响。最后针对微生物固碳的关键共性技术难点,简要展望了可行性的解决方案及相关应用前景。     

Efficient molecular cloning of environmental DNA from geothermal sediments

An efficient and simple method for constructing an environmental library using mechanically sheared DNA obtained directly from geothermal sediments is presented. The method is based on blunt-end modification of DNA fragments followed by 3-adenylation using Vent DNA polymerase and Taq DNA polymerase, respectively. The prepared DNA fragments are then ligated into a TA cloning vector and used in the transformation of Escherichia coli. This method has been successfully applied to the cloning of ORFs derived from uncultivated prokaryotes present in geothermal sediment.     

古菌在红树林沉积物中的多样性及其碳代谢机制

红树林湿地生态系统具有维持生物多样性、净化环境及维持海岸带生态平衡等多种功能。古菌普遍存在于红树林沉积物中,在元素的生物地球化学循环中发挥着重要作用。古菌具有丰富的碳代谢多样性,能固定CO_2,参与甲烷循环,产乙酸,降解蛋白质、多聚碳水化合物等有机质,但目前对于红树林沉积物中古菌碳代谢的研究才刚刚起步。高通量测序技术的快速发展促进了大量新的古菌门类的发现,这些新的古菌门类具备多样的碳代谢潜力。本文简要概述古菌的主要类群与分布,综述国内外有关古菌碳代谢多样性的最新研究进展,并阐明这些古菌在红树林生态系统中的生态分布和功能特征,为进一步探究古菌代谢机制提供知识基础。     

Bioturbation enhances the aerobic respiration of lake sediments in warming lakes

While lakes occupy less than 2% of the total surface of the Earth, they play a substantial role in global biogeochemical cycles. For instance, shallow lakes are important sites of carbon metabolism. Aerobic respiration is one of the important drivers of the carbon metabolism in lakes. In this context, bioturbation impacts of benthic animals (biological reworking of sediment matrix and ventilation of the sediment) on sediment aerobic respiration have previously been underestimated. Biological activity is likely to change over the course of a year due to seasonal changes of water temperatures. This study uses microcosm experiments to investigate how the impact of bioturbation (by Diptera, Chironomidae larvae) on lake sediment respiration changes when temperatures increase. While at 5°C, respiration in sediments with and without chironomids did not differ, at 30°C sediment respiration in microcosms with 2000 chironomids per m² was 4.9 times higher than in uninhabited sediments. Our results indicate that lake water temperature increases could significantly enhance lake sediment respiration, which allows us to better understand seasonal changes in lake respiration and carbon metabolism as well as the potential impacts of global warming.     

Microdistribution of sulfate-reducing bacteria in sediments of a hypertrophic lake and their response to the addition of organic matter

To clarify the ecological significance of the association of sulfate-reducing bacteria (SRB) with sediment particle size, SRB utilizing lactate (l-SRB), propionate (p-SRB) and acetate (a-SRB) were examined with different sizes of sediment particles in a hypertrophic freshwater lake using the anaerobic plate count method. The numbers ofl-SRB anda-SRB were 10⁴–10⁵ colony forming units (CFU) per ml in the 0–3 cm layer and 10²–10³ CFU ml⁻¹ in the 10–13 cm layer while the numbers ofp-SRB were one or two orders lower than those ofl-SRB anda-SRB. A sediment suspension was fractionated into four fractions (<1, 1–10, 10–94 and >94 μm). The highest proportions ofl-SRB anda-SRB were found in the 10–94 μm fraction: 66–97% forl-SRB and 53–98% fora-SRB. The highest proportion ofp-SRB was found in the >94 μm fraction (70–74%). These results indicate that most SRB were associated with sediment particles. One isolate from an acetate-utilizing enrichment culture was similar toDesulfotomaculum acetoxidans, a spore-forming sulfate-reducing bacterium. When lactate and sulfate were added to sediment samples,l-SRB anda-SRB in the <10 μm-fraction grew more rapidly than those in whole sediment for the first 2 days. This result suggests that nutrients uptake by free-living and small particle-associated (<10 μm) SRB is higher than that by SRB associated with larger particles.     

Legume species identity and soil nitrogen supply determine symbiotic nitrogen-fixation responses to elevated atmospheric [CO2

In nitrogen (N)-limited systems, the response of symbiotic N fixation to elevated atmospheric [CO2] may be an important determinant of ecosystem responses to this global change. Experimental tests of the effects of elevated [CO2] have not been consistent. Although rarely tested, differences among legume species and N supply may be important. In a field free-air CO2 enrichment (FACE) experiment, we determined, for four legume species, whether the effects of elevated atmospheric [CO2] on symbiotic N fixation depended on soil N availability or species identity. Natural abundance and pool-dilution 15N methods were used to estimate N fixation. Although N addition did, in general, decrease N fixation, contrary to theoretical predictions, elevated [CO2] did not universally increase N fixation. Rather, the effect of elevated [CO2] on N fixation was positive, neutral or negative, depending on the species and N addition. Our results suggest that legume species identity and N supply are critical factors in determining symbiotic N-fixation responses to increased atmospheric [CO2].     

Reconstructing long‐term changes (150 years) in the carbon cycle of a clear‐water lake based on the stable carbon isotope composition (δ13C) of chironomid and cladoceran subfossil remains

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A unifying conceptual model for the environmental responses of isoprene emissions from plants

Background and Aims

Isoprene is the most important volatile organic compound emitted by land plants in terms of abundance and environmental effects. Controls on isoprene emission rates include light, temperature, water supply and CO₂ concentration. A need to quantify these controls has long been recognized. There are already models that give realistic results, but they are complex, highly empirical and require separate responses to different drivers. This study sets out to find a simpler, unifying principle.

Methods

A simple model is presented based on the idea of balancing demands for reducing power (derived from photosynthetic electron transport) in primary metabolism versus the secondary pathway that leads to the synthesis of isoprene. This model''s ability to account for key features in a variety of experimental data sets is assessed.

Key results

The model simultaneously predicts the fundamental responses observed in short-term experiments, namely: (1) the decoupling between carbon assimilation and isoprene emission; (2) a continued increase in isoprene emission with photosynthetically active radiation (PAR) at high PAR, after carbon assimilation has saturated; (3) a maximum of isoprene emission at low internal CO₂ concentration (c_i) and an asymptotic decline thereafter with increasing c_i; (4) maintenance of high isoprene emissions when carbon assimilation is restricted by drought; and (5) a temperature optimum higher than that of photosynthesis, but lower than that of isoprene synthase activity.

Conclusions

A simple model was used to test the hypothesis that reducing power available to the synthesis pathway for isoprene varies according to the extent to which the needs of carbon assimilation are satisfied. Despite its simplicity the model explains much in terms of the observed response of isoprene to external drivers as well as the observed decoupling between carbon assimilation and isoprene emission. The concept has the potential to improve global-scale modelling of vegetation isoprene emission.     

Different patterns of phosphorus release from lake sediments in laboratory experiments

The phosphorus release from surface sediments of eight lakes, mainly shallow lakes in agricultural areas, was studied in laboratory batch experiments with additions of acetate and/ or nitrate. The lake sediments could be separated into three categories. Some sediments did not release phosphorus under any conditions. The second category showed a high phosphorus release rate when acetate was added, in order to stimulate bacterial activity and oxygen consumption. The addition of nitrate, only, stabilized the redox conditions and prevented phosphorus release. This pattern followed the classical theories of Einsele and Mortimer. The third sediment category released phosphorus up to some level which remained constant throughout the experiment, and was independent of acetate and/or nitrate additions.Several extraction procedures and adsorption-desorption experiments were performed in order to characterize the sediment phosphorus and thus explain the different behaviours of the three sediment categories.