The changing role of terrestrial and autochthonous organic matter in newly flooded lakes

Examination of the gut contents of mud-dwelling animals in three newly flooded lakes shows terrestrial organic matter to be a major component, particularly during filling of the lake basin. After filling is complete, a fall-off in total biomass of fauna is usually accompanied by significant reduction in the proportion of terrestrial detritus in favour of algal food. It is concluded that newly formed lakes pass through two phases. During flooding they are dependent on the terrestrial ecosystem. This is followed by a switch, immediately after filling, to more self-sustained autochthonous-based food chains.     

Metagenomics of microbial and viral life in terrestrial geothermal environments

Geothermally heated regions of Earth, such as terrestrial volcanic areas (fumaroles, hot springs, and geysers) and deep-sea hydrothermal vents, represent a variety of different environments populated by extremophilic archaeal and bacterial microorganisms. Since most of these microbes thriving in such harsh biotopes, they are often recalcitrant to cultivation; therefore, ecological, physiological and phylogenetic studies of these microbial populations have been hampered for a long time. More recently, culture-independent methodologies coupled with the fast development of next generation sequencing technologies as well as with the continuous advances in computational biology, have allowed the production of large amounts of metagenomic data. Specifically, these approaches have assessed the phylogenetic composition and functional potential of microbial consortia thriving within these habitats, shedding light on how extreme physico-chemical conditions and biological interactions have shaped such microbial communities. Metagenomics allowed to better understand that the exposure to an extreme range of selective pressures in such severe environments, accounts for genomic flexibility and metabolic versatility of microbial and viral communities, and makes extreme- and hyper-thermophiles suitable for bioprospecting purposes, representing an interesting source for novel thermostable proteins that can be potentially used in several industrial processes.     

极地陆域微生物多样性研究进展

极地是指高纬度、高海拔地区,包括南极(60°S以南)、北极(60°N以北)和被称为“第三极”的青藏高原地区(平均海拔4,500 m).这些地区气温极低、养分极度贫乏,生态系统非常脆弱,对全球气候变化极为敏感,该地区生态系统一旦破坏将很难恢复.尽管极地地区自然条件恶劣,但在这些极端环境中栖息着大量微生物,是元素生物地球化学循环的主要驱动者,对极地生态系统的构建和维持具有非常重要的作用.本文综述了极地土壤、湖泊和冰川等陆域环境微生物研究进展.在这些极地环境中,目前已发现了Acidobacteria,Actinobacteria,Bacteroidetes,Cyanobacteria和Firmicutes等类群,这些微生物具有嗜盐/耐盐及耐低温等特征.我国在极地微生物生态学研究方面落后于发达国家,建议优先发展较易到达的青藏高原地区微生物生态学长期定位观测,这将有助于较快提升我国极地微生物多样性研究水平,深入了解极端生命过程及其生态学效应.     

Cenomanian-Turonian carbon isotope events recorded in terrestrial organic matter from northern Japan

Carbon isotopic fluctuations recorded in terrestrial organic matter from the Upper Cretaceous Cenomanian-Turonian succession of Hokkaido, Japan show a remarkably similar pattern to isotopic fluctuation in carbonate carbon reported from southern England and the Italian Apennines. Chronological correlation for the Cenomanian-Turonian section of Japan is based on planktonic foraminiferal biostratigraphy with some additional data from macrofossils, allowing a detailed comparison of isotope stratigraphies for Japan and Europe. Three distinct features of the isotope profile, namely a positive spike near the Cenomanian/Turonian boundary, a shoulder in the lower-middle Turonian and a level segment in the middle-upper Turonian are observed in Japan. These features are biostratigraphically comparable and correlative with isotope profiles reported from Europe. The single factor influencing isotopic composition of both terrestrial organic carbon and marine carbonate carbon is isotopic change in the global CO₂ reservoir of the ocean-atmosphere system. If these three carbon isotope features are synchronous, they may be inferred as having been caused by global phenomena and as providing global high-resolution chemo-stratigraphic markers. Carbon isotope stratigraphy could be an important bridge between terrestrial inland sequences and marine sequences.     

Variations in microbial isotopic fractionation during soil organic matter decomposition

The soil microbial biomass (SMB) is known to participate in key soil processes such as the decomposition of soil organic matter (SOM). However, its contribution to the isotopic composition of the SOM is not clear yet. Shifts in the ¹³C and ¹⁵N natural abundances of the SMB and SOM fractions (mineralised, water soluble and non-extractable) were investigated by incubating an unamended arable soil for 6 months. Microbial communities were also studied using Fatty Acid Methyl Ester specific isotope analysis. The SMB was significantly ¹³C and ¹⁵N-enriched relative to other fractions throughout the incubation. However, significant isotopic variations with time were also observed due to the rapid consumption of relatively ¹³C-enriched water soluble compounds. The increase in the difference in SMB and water soluble ¹⁵N compositions as the water soluble C/N ratio decreased, indicated a shift from N assimilation to N dissimilation during the incubation. These changes also induced modifications of the microbial community structure. Once the system reached a steady-state (after 1 month), the isotopic trends appeared to corroborate those obtained in long term experiments in the field in that there was a constant microbial isotopic fractionation leading to a ¹³C and ¹⁵N enrichment of the SOM over the long-term. This work also suggests that caution must be exercised when interpreting short term incubation studies since perturbations associated with experimental set-up can have an important effect on C and N dynamics, microbial fractionation of ¹³C and ¹⁵N and microbial community structure.     

Heterotrophic microbial activity and organic matter degradation in coastal lagoons of Colombia

In this study we measured the community respiration and the bacterial respiration as part of the overall degradation process of organic material. Additionally, the turnover rates of the pools of dissolved free glucose and acetate as representatives of the fraction of easily degradable low molecular organic solutes were determined. The study was performed in several coastal lagoons of the "Outer Delta of the Río Magdalena" in northern Colombia. The lagoons can be separated into two groups: The first group contains highly productive brackish lagoons with chl a concentrations ranging from 62-130 micrograms/l. The second group consists of less productive freshwater lagoons with chl a between 5.5-19 micrograms/l. Turnover rates of glucose and acetate were very fast in the highly productive lagoons resulting in turnover times of less than 20 min for both compounds. In the less productive systems the cycling of glucose and acetate was much slower. Here the mean values of the turnover times were 2 hr for glucose and 1.5 hr for acetate. The rates of bacterial DNA-formation measured as thymidine incorporation differed significantly between both groups of lagoons, being very high (1.86-2.76 nmol/l/hr) in the highly productive and relatively low (0.073-0.55 nmol/l/hr) in the less productive group. Water column community respiration ranged between 122 and 16 micrograms C/l/hr with means of 88 micrograms C/l/hr in the highly and 19 micrograms C/l/hr in the less productive group. In the first group the mean values of the bacterial contribution to community respiration amounted to 37% and in the second group to 18%. The bacterial respiration was determined in an indirect way via bacterial biomass production and assuming a growth efficiency of 50%. It is discussed whether this relatively high growth efficiency allows reasonable results in both groups of lagoons.     

Characterisation of organic matter from anaerobic digestion of organic waste by aerobic microbial activity

The aim of this study was to examine whether the characterisation of organic matter on the basis of an oxygen uptake rate (OUR) could be applied to organic waste from an anaerobic waste treatment process. Three anaerobic digestion experiments were carried out in a bioreactor. Volatile fatty acids (VFA) and dissolved organic carbon (DOC) were monitored. OUR-experiments were carried out with diluted samples from the process. The graphs of the OUR-experiments showed a clear lag-phase, which was due to the slow adaptation of aerobic microorganisms. Model simulations of the OUR versus time curve showed sufficient agreement, if based on one fraction of readily biodegradable and two fractions of less easily biodegradable organic matter. The shape of the simulated graphs was affected considerably by the value of the maintenance energy requirement rate qm and could be improved by reducing the standard value qm = 1 d(-1) to qm = 0.1 d(-1). Only little agreement was achieved when comparing the results of the OUR-experiments with the VFA- and DOC-concentrations. Experiments with additional trace elements and vitamins led to an increase in the OUR and proved that the oxygen consumption was not exclusively determined by the availability of organic matter.     

The role of organic matter in soil manganese equilibrium

Summary Tests were conducted to determine the role of additions of fresh organic matter (ground cotton seed hulls) to an alluvial loam soil of pH 8 on manganese equilibrium. It was shown that organic matter has a reducing potential which, when added to the soil, resulted in a rapid and marked increase in exchangeable manganese. The reduction is enhanced by higher temperatures (21.1vs 37.7°C) and additions of water (field capacityvs air dry) and incubation periods up to 3 days. It is suggested that the shift in the soil manganese equilibrium, induced by such factors as waterlogging or anaerobic conditions, will be more pronounced when soils contain high levels of organic matter.Patterns of the standard deviations of sample exchangeable manganese data within treatments showed that the variance is highest in moist soil, lower concentrations of added organic matter, and at longer durations of incubation. Re-oxidation of manganese occurred at lower levels of added organic matter (2 and 4%) and extended incubation time (5 to 9 days).The investigation reported in this paper (67-10-36) is in connection with a project of the Kentucky Agricultural Experiment Station and is published by permission of the Director.     

The role of organic matter and microbial community controlling nitrate reduction under elevated ferrous iron concentrations in boreal lake sediments

Hydrobiologia - The nitrogen availability, that affects the greenhouse gas emission and the trophic level of lakes, is controlled mainly by microbial processes. We measured in a boreal nitrate and...     

Temporal shift in contribution of terrestrial organic matter to consumer production in a grassland river

1. We used stable isotopes to study the temporal (early summer versus autumn) pattern of use of terrestrial and aquatic sources of organic carbon by consumers in two bedrock‐confined reaches of a grassland river in New Zealand.
2. The major sources of organic carbon available to primary consumers were expected to be terrestrial leaf‐litter and biofilm from the stream channel. These putative carbon sources showed no significant change in mean δ¹³C between summer and autumn. Leaf litter (mean δ¹³C13C compared to biofilm (mean δ¹³C>?19.92).
3. In contrast to leaf litter and biofilm, the δ¹³C of consumers changed over time, being enriched in ¹³C in the autumn compared with early summer. Both the magnitude (>5‰ in some cases) and rapidity of this shift (< 3 months) was surprising.
4. A two‐source mixing model indicated that, during early summer, terrestrial carbon comprised> 50% of tissue carbon for 15 of the 17 taxa of aquatic consumers analysed. During autumn, terrestrial carbon comprised> 50% of the tissue carbon of only five of 25 taxa. Because the mean δ¹³C of putative food sources was consistent over time, the shift in δ¹³C values for consumers is attributed to a change in relative amounts of terrestrial and aquatic carbon available for consumption.
5. Because seston consists of a mixture of many particles of diverse origin, it may provide an integrated measure of catchment‐wide sources of organic matter entering a stream channel. Like the tissues of most consumers, mean δ¹³C values for seston showed a significant shift toward ¹³C enrichment. This indicated that the relative availability of terrestrial carbon decreased from summer to autumn.
6. The actual quantity of carbon contributed to the stream food‐web by this potential terrestrial–aquatic link is unknown. Although terrestrial carbon may comprise a high proportion of the tissue carbon of consumers prior to summer, the majority of secondary production (and carbon sequestration) probably occurs during early summer as a consequence of rising temperature and high quality food in the form of biofilm.     

Quantifying microbial control of soil organic matter dynamics at macrosystem scales

Biogeochemistry - Soil organic matter (SOM) stocks, decomposition and persistence are largely the product of controls that act locally. Yet the controls are shaped and interact at multiple...     

Enzymic and molecular analysis of microbial communities associated with lotic particulate organic matter

1. Most allochthonous plant detritus moves through stream ecosystems as fine particulate organic matter (FPOM), whose associated microbial communities, unlike those of coarse detritus, have received little scrutiny. 2. Benthic POM was collected from a fourth-order boreal river and two first-order tributaries in northern New York during July 1991, sorted it into eight size fractions ranging from 38 to >4000 μm, and assayed each fraction for ergosterol, DNA, and the activity of nine extracellular enzymes: β-1, 4-glucosidase, endocellulase, cellobiohydrolase, phenol oxidase, peroxidase, β-N-acetylglucosaminidase, acid phosphatase, alkaline phosphatase, and aryl sulphatase. In addition, DNA-DNA hybridization was used to investigate the structural similarity of the microbial communities associated with the FPOM fractions. 3. Various enzymes showed distinct activity patterns in relation to particle size as well as among sites. Half of the possible pairwise correlations among enzyme variables were statistically significant, but no enzyme activities were correlated with biomass indices (DNA and ergosterol concentration). DNA-DNA dot-blot hybridizations suggested extensive structural similarity among the microbial communities associated with FPOM fractions. 4. Cluster analysis was used to compare microbial functional similarity, measured by enzyme assays, and structural similarity, measured by DNA—DNA hybridization. Comparison of cluster coefficients showed a weak correlation between community structural similarity and functional similarity (r= 0.51) with fifteen of eighteen fractions grouped within a narrow range of distance. 5. The results suggest a convergence in microbially mediated FPOM processing despite system-level differences in litter and water quality.     

Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics

Stratified sulfurous lakes are appropriate environments for studying the links between composition and functionality in microbial communities and are potentially modern analogs of anoxic conditions prevailing in the ancient ocean. We explored these aspects in the Lake Banyoles karstic area (NE Spain) through metagenomics and in silico reconstruction of carbon, nitrogen and sulfur metabolic pathways that were tightly coupled through a few bacterial groups. The potential for nitrogen fixation and denitrification was detected in both autotrophs and heterotrophs, with a major role for nitrogen and carbon fixations in Chlorobiaceae. Campylobacterales accounted for a large percentage of denitrification genes, while Gallionellales were putatively involved in denitrification, iron oxidation and carbon fixation and may have a major role in the biogeochemistry of the iron cycle. Bacteroidales were also abundant and showed potential for dissimilatory nitrate reduction to ammonium. The very low abundance of genes for nitrification, the minor presence of anammox genes, the high potential for nitrogen fixation and mineralization and the potential for chemotrophic CO₂ fixation and CO oxidation all provide potential clues on the anoxic zones functioning. We observed higher gene abundance of ammonia-oxidizing bacteria than ammonia-oxidizing archaea that may have a geochemical and evolutionary link related to the dominance of Fe in these environments. Overall, these results offer a more detailed perspective on the microbial ecology of anoxic environments and may help to develop new geochemical proxies to infer biology and chemistry interactions in ancient ecosystems.     

Post-fire effects of soil heating intensity and pyrogenic organic matter on microbial anabolism

Biogeochemistry - Wildfires cause direct and indirect CO2 emissions due to combustion and post-fire decomposition. Approximately half of temperate forest carbon (C) is stored in soil, so post-fire...     

Oxidoreductases and cellulases in lichens: Possible roles in lichen biology and soil organic matter turnover

Lichens are symbiotic associations of a fungus (usually an Ascomycete) with green algae and/or a cyanobacterium. They dominate on 8 % of the world's land surface, mainly in Arctic and Antarctic regions, tundra, high mountain elevations and as components of dryland crusts. In many ecosystems, lichens are the pioneers on the bare rock or soil following disturbance, presumably because of their tolerance to desiccation and high temperature. Lichens have long been recognized as agents of mineral weathering and fine-earth stabilization. Being dominant biomass producers in extreme environments they contribute to primary accumulation of soil organic matter. However, biochemical role of lichens in soil processes is unknown. Our recent research has demonstrated that Peltigeralean lichens contain redox enzymes which in free-living fungi participate in lignocellulose degradation and humification. Thus lichen enzymes may catalyse formation and degradation of soil organic matter, particularly in high-stress communities dominated by lower plants. In the present review we synthesize recently published data on lichen phenol oxidases, peroxidases, and cellulases and discuss their possible roles in lichen physiology and soil organic matter transformations.     

Soil microbial diversity affects soil organic matter decomposition in a silty grassland soil

Soil microorganisms play a pivotal role in soil organic matter (SOM) turn-over and their diversity is discussed as a key to the function of soil ecosystems. However, the extent to which SOM dynamics may be linked to changes in soil microbial diversity remains largely unknown. We characterized SOM degradation along a microbial diversity gradient in a two month incubation experiment under controlled laboratory conditions. A microbial diversity gradient was created by diluting soil suspension of a silty grassland soil. Microcosms containing the same sterilized soil were re-inoculated with one of the created microbial diversities, and were amended with ¹³C labeled wheat in order to assess whether SOM decomposition is linked to soil microbial diversity or not. Structural composition of wheat was assessed by solid-state ¹³C nuclear magnetic resonance, sugar and lignin content was quantified and labeled wheat contribution was determined by ¹³C compound specific analyses. Results showed decreased wheat O-alkyl-C with increasing microbial diversity. Total non-cellulosic sugar-C derived from wheat was not significantly influenced by microbial diversity. Carbon from wheat sugars (arabinose-C and xylose-C), however, was highest when microbial diversity was low, indicating reduced wheat sugar decomposition at low microbial diversity. Xylose-C was significantly correlated with the Shannon diversity index of the bacterial community. Soil lignin-C decreased irrespective of microbial diversity. At low microbial diversity the oxidation state of vanillyl–lignin units was significantly reduced. We conclude that microbial diversity alters bulk chemical structure, the decomposition of plant litter sugars and influences the microbial oxidation of total vanillyl–lignins, thus changing SOM composition.