The spatial distribution of archaeal lipids in a mesoscale subtropical watershed,Southeast China

Archaea play an important role in global carbon and nitrogen cycles. Archaeal lipids, such as isoprenoid glycerol diakyl glycerol tetraethers (iGDGTs), are important biomarkers tracing change in archaeal community structure and biogeochemical processes in the natural environments. In this research, the spatial distributions of archaeal lipids in the surface sediments of the Jiulong River (JR) and the Jiulong River estuary (JRE) were examined. GDGT-0 (containing zero cyclopentyl ring) and crenarchaeol were the most abundant iGDGTs in the JR and JRE. From the rivers to the estuary, the total iGDGTs, GDGT-0, crenarchaeol and archaeol concentrations showed significant spatial variation; in particular, GDGT-0 and archaeol in the river may be predominantly derived in situ from methanogens, whereas crenarchaeol in the estuary mainly derived in situ from Thaumarchaeota. We inferred that archaeal community was dominated by methanogens in the Jiulong River and by Thaumarchaeota in the Jiulong River estuary, which are consistent with change in archaeal community structure observed in other estuarine environments.     

淡水蓝藻的高温适应

本文在有关文献的基础上综合分析了淡水蓝藻对高温的适应,并对淡水蓝藻高温适应机制提出了几种看法。生长在高温中的淡水蓝藻有这样一些特点:（1）不同种类对高温的适应机制稍有不同;（2）类囊体膜具有较高的稳定性;（3）藻体在受热时产生热休克蛋白以保护细胞内的酶免于热变性;（4）光合作用系统具有热稳定性;（5）DNA具有热稳定性;（6）蛋白质的合成系统具有热稳定性。其中DNA和光合作用系统的热稳定性起着关键的作用,热休克蛋白的产生和类囊体膜中脂肪酸的饱和程度是在基因水平上调控的。     

Bio-Organic Geochemistry research in China: Advances,opportunities and challenges

The discipline of “Bio-Organic Geochemistry” is a cross research field between biogeochemistry and traditional organic geochemistry, which focuses on geochemical processes related to the biosynthesis of organic molecules (particularly lipids) by (micro) organisms, organic matter production by primary producers, degradation of organic matter by microbial processes recorded by retainable lipid biomarkers, and organic proxies for studies of paleo-climate, paleo-environments, paleoecology and Earth evolution. This field aims to go beyond the traditional petroleum-oriented Organic Geochemistry by integrating with biogeochemical concepts concerned mostly with biomolecules from cellular material such as DNA and lipids. A formal Chinese organization in Bio-Organic Geochemistry was established in 2012 when the first conference was held in Guangzhou. This organization has witnessed rapid growth over the past six years with focused research addressing organic proxies in paleoclimate and paleoenvironmental applications, with particular rapid development in glycerol dialkyl glycerol tetraethers-derived proxies. Most progresses in China so far are made following or paralleling the international trend in biogeochemical studies. Things have begun to change with China’s ambitious initiatives in several bio-geo programs such as the Ocean Deep Drilling Program of China, the Microbial Hydrosphere Program, the Deep Carbon Observatory, and the Microbiome Program. Looking forward in the 21st Century, the growing Chinese research community in Bio-Organic Geochemistry faces grand opportunities and challenges as Chinese scientists propel themselves toward global research frontiers.     

New approaches for archaeal genome-guided cultivation

Archaea, one of the three domains of life along with Bacteria and Eukarya, contains ancient life forms such as methanogen that are observed today on Earth, and one lineage Asgard archaea is also considered the closest ancestor of Eukarya.Recently, with the development of interdisciplinary studies from Earth and Life sciences, archaeal organisms are considered to play pivotal roles in geochemical cycling in nature. However, our understanding of the attributes, origin and evolution, geochemical and ecological functions of Archaea is hampered by the scarcity of archaeal isolates, which has represented a challenge to researchers for the last 40 years. Cultivation-independent sequencing and phylogenomic analyses have demonstrated a considerable diversity of Archaea with more than 20 novel phyla. However, only four archaeal phyla have cultured representatives, leaving large gaps in our knowledge of the metabolic capabilities and ecological functions of the majority of archaeal strains identified exclusively by DNA sequencing. In this review, we summarize the discovery and development of archaeal research, highlight the knowledge gap between uncultured and cultured archaeal microbes, and call on the importance of devoting greater research efforts to archaeal cultivation. Finally, we outlined new ideas and strategic approaches, namely,(1)genome-based methods,(2) microbial network information-based methods,(3) genome-scale model-guided methods, and(4)machine learning methods, to enable the cultivation of uncultivated archaeal microbes using accumulated high-throughput sequencing data.     

湖泊水体微生物四醚膜脂化合物研究进展

来源于微生物膜脂的甘油二烷基甘油四醚类(GDGTs)化合物是近年来被广泛用于古环境定量重建研究的化合物之一,究其原因在于此类化合物对环境响应敏感,特别是温度与pH值等,据此而建立的一系列GDGTs指标有效定量重建海洋、湖泊、泥炭以及土壤等不同沉积载体的环境信息.目前已在全球范围广泛开展湖泊沉积物GDGTs的研究工作,相继建立的全球以及不同区域尺度的湖泊沉积物GDGTs校正方程,已被用于湖泊古环境的定量重建研究,有效记载古湖泊环境变迁信息.相较之下,基于湖泊水体GDGTs的调查工作则起步较晚,但越来越多的研究显示,不同类型湖泊水体普遍贡献GDGTs,然而究竟此类水生来源GDGTs是否与陆源以及湖泊沉积物GDGTs具有类似的分布,以及他们对环境因素的响应如何,这都为湖泊古温度定量重建研究带来不确定性.基于此,本文总结这10年来湖泊水体GDGTs研究工作的进展,首先阐述湖泊水体不同来源(古菌以及细菌)GDGTs的分布情况,研究发现水体不同层位GDGTs浓度以及各组分之间存在差异,并且水深在不同湖泊对GDGTs浓度以及各组分相对比例的影响存在差异.此外还总结湖泊水体中古菌来源isoGDGTs以及细菌来源brGDGTs的生物来源,并进一步分析环境因素对不同深度水体GDGTs分布的影响,虽然温度依然是影响水体中GDGTs分布的首要因素之一,然而湖泊水深、温度以及水体中溶解氧浓度等因素存在着一定的耦合关系,这些因素往往协同作用于水体GDGTs,因此会为评估环境因素对水体GDGTs的影响带来难度.     

Seasonal variations of physiological and cellular biomarkers and their use in the biomonitoring of north Adriatic coastal waters (Croatia)

Lysosomal membrane stability, the content of neutral lipids and lipofuscin as cellular biomarkers were measured in the digestive gland of mussels, Mytilus galloprovincialis Lam., during a one year survey at selected sites along the coast of the northern Adriatic. The ability of mussels to survive in air as a general physiological response was tested at the same sites. Annual changes of sea temperature, salinity, O(2) saturation, pH and chlorophyll a concentration were measured and the effects of these environmental factors on the biomarkers selected for this study were determined. Survival of mussels after aerial exposure was significantly (p < 0.05) reduced in mussels collected from the contaminated harbors of Pula and Rijeka compared to clean control sites. Lysosomal membrane stability of mussels from urban and industrial areas was also lower indicating exposure to different environmental contaminants. At the same sites, the content of neutral lipids and lipofuscin in digestive cells was significantly higher compared to the reference sites, suggesting alterations in lipid metabolism and contaminant-induced peroxidation of cell membranes. The greatest influence of natural environmental factors was observed for the aerial survival of mussels and the neutral lipids and lipofuscin content in the digestive gland, indicating that the annual cycles of biomarker responses should be well understood for a correct interpretation of biomonitoring results.     

Environmental impacts on the distribution of microbial tetraether lipids in Chinese lakes with contrasting pH: Implications for lacustrine paleoenvironmental reconstructions

Glycerol dialkyl glycerol tetraethers(GDGTs) in lake sediments are useful biomarkers for the continental paleoclimatic reconstruction. However, the environmental controls on the distribution of these compounds, in particular the 6-methyl isomers of bacterial branched GDGTs(bGDGTs), in the lakes with contrasting pH, are still unknown, hindering their application for paleo-reconstructions. Here, we investigated the environmental impacts on the distribution of GDGTs in 17 alkaline lakes and 1 acid lake in China. It was found that the dissolved oxygen content in water column may have an impact on the distribution of archaeal isoprenoid GDGTs(iGDGTs) by causing the change in archaeal communities. The ratio of GDGT-0/crenarchaeol increases with decreasing oxygen content, indicating that the relative abundance of anaerobic methanogenic archaea or Miscellaneous Crenarchaeotic Group(MCG) vs. aerobic Thaumarchaeota is controlled by the oxygen content dissolved in water of these lakes. Thaumarchaeota are likely to contribute only a small proportion of iGDGTs in the relatively oxygen-depleted lakes, and thus TEX_(86) is not suitable for the reconstruction of the surface temperature of these lakes. The abundance ratio of iGDGTs to bGDGTs(R_(i/b)) appears to show no relationship with water pH in all the lakes, but exhibits a significant positive correlation with the water depth of the acid Lake Qinghai in Tengchong. As expected, the methylation degree of bGDGTs(MBT′) was found to correlate with both mean annual air temperature(MAT) and water pH, and the cyclization degree of bGDGTs(CBT) correlates only with water pH in these lakes. However, the MBT′_(5ME), an index to measure the methylation degree of 5-methyl bGDGTs, exhibits no relationship with MAT, whereas MBT′_(6ME), the methylation degree of 6-methyl bGDGTs, was found to correlate significantly with MAT. This is opposite to the situation observed in the global soils, pointing to a different adaptation of b GDGT-producing bacteria to environmental variables or different microbial sources of bGDGTs in these lakes. The relative abundance of 6- vs. 5-methyl bGDGTs is controlled by pH in these lakes, similar to that observed in worldwide soils. Hence, the isomer ratio(IR) of 6-methyl bGDGTs or CBT′ can be used as a proxy for water pH, although they might be influenced by other environmental factors including temperature in the lakes with a narrow range of pH.     

Archaea,the tree of life,and cellular evolution in eukaryotes

The early history of life harbours many unresolved evolutionary questions, none more important than the genomic origin and cellular evolution of eukaryotes. An issue central to eukaryote origin concerns the position of eukaryotes in the tree of life and the relationship of the host lineage that acquired the mitochondrion some two billion years ago to lineages of modern-day archaea. Recent analyses indicate that the host lineage branches within the Archaea, prompting the search for novel archaeal lineages that can improve our understanding of the cellular evolution of eukaryotes. Here we give a brief review of the studies on Archaea, the tree of life and the cellular evolution of eukaryotes, which is followed by an overview of recent progress fueled by new genomic technologies and recent status of archaeal research in China. Future directions for the study of early evolution are considered.     

Vertical distribution of bacteria and archaea in a CO2-rich meromictic lake: A case study of Lake Monoun

In order to assess the diversity and spatial distribution of bacterial and archaeal communities in a CO₂-rich and meromictic lake, samples were collected along the water column of Lake Monoun and analyzed using PCR-DGGE and quantitative analyses of the 16S rRNA gene. The retrieved sequences were affiliated to 6 bacterial phyla and two archaeal phyla which plausible environmental functions map with the physico-chemical parameters of the lake. Unclassified sequences were also detected. This suggests heterogeneity in community composition and existence of potential candidate divisions. For instance, amongst the bacterial sequences, 18.2% matched with methanotrophic bacteria of the order methylococcales and amongst the archaeal sequences, 16.6% matched with methanogenic species of the order methanomicrobiales. Hence, evidencing the existence of methane-related prokaryotes in the lake, a finding that would play a key role in our understanding of the methane puzzle of Lake Monoun. Other groups capable of a wide range of metal and nutrients transformations were also detected, as well as those of unknown functions. The layering of microbial communities also appeared to directly or indirectly depend on oxygen availability. DGGE and qPCR analyses both suggested a scarcity of archaea in the surface samples. Furthermore, qPCR revealed that bacteria were numerically more important than archaea in all the samples. The general distribution along the water column indicated that archaeal abundance increases with depth.     

What is wrong with post-fire soil erosion modelling? A meta-analysis on current approaches,research gaps,and future directions

In the near future, a higher occurrence of wildfires is expected due to climate change, carrying social, environmental, and economic implications. Such impacts are often associated with an increase of post-fire hydrological and erosive responses, which are difficult to predict. Soil erosion models have been proven to be a valuable tool in the decision-making process, from emergency response to long-term planning, however, they were not designed for post-fire conditions, so need to be adapted to include fire-induced changes. In recent years, there have been an increasing number of studies testing different models and adaptations for the prediction of post-fire soil erosion. However, many of these adaptations are being applied without field validation or model performance assessment. Therefore, this study aims to describe the scientific advances in the last 20 years in post-fire soil erosion modelling research and evaluate model adaptations to burned areas that aim to include: (i) fire-induced changes in soil and ground cover; (ii) fire-induced changes in infiltration; (iii) burn severity; and (iv) mitigation measures in their predictions. This study also discusses the strengths and weaknesses of these approaches, suggests potential improvements, and identifies directions for future research. Results show that studies are not homogeneously distributed worldwide, according to the model type used or by region most affected by wildfire. During calibration, 73% of cases involved model adaptation to burned conditions, and only 21% attempted to accommodate new processes. Burn severity was addressed in 75% of cases, whilst mitigation measures were simulated in 27%. Additionally, only a minor percentage of model predictions were validated with independent field data (17%) or assessed for uncertainties (13%). Therefore, further efforts are required in the adaptation of erosion models to burned conditions, to be widely used for post-fire management decisions. © 2020 John Wiley & Sons, Ltd.     

Physiological and genetical adaptation to temperature in fish populations

The physiological and genetical adaptation of fishes to environmental temperatures has been studied by analyzing data concerning: (i) the oxygen binding properties of haemoglobin recorded during growth experiments on Atlantic cod, and (ii) the primary structure of haemoglobin (Hb) and lactate dehydrogenase (LDH) of several fish species living in polar and temperate areas. The results on the oxygen binding properties of cod's haemoglobin indicate that for this species a temperature of around 12°C is the most favourable one, irrespective of the haemoglobin genotype, and are in line with recent evidence challenging the existence of significant evolutionary differences between cod stocks in North Atlantic. The primary structures of both Hb and LDH from species living under temperate environments show a higher variability as compared to that from polar species, although the difference in the recurrent patterns of hydrophobicity between the two areas is much larger for Hb. These results highlight the dominant role of physiological and genetical factors in shaping the adaptation to temperature at the individual and at the species level, respectively.     

Seasonal variations of biomarker responses in the marine blue mussel (Mytilus spp.)

Biomarkers, which can detect changes at the biochemical level, have been used for many years as early warning tools in environmental monitoring. In order to distinguish between natural variability and the potential effects of anthropogenic pollution, it is essential to identify background levels and establish the potential influence of abiotic (season, temperature and salinity) and biotic (gametogenesis) factors. In this study, we examined various biomarkers of stress (glutathione S-transferase (GST)), reproduction (vitellin-like proteins) and damage (lipid peroxidation (LPO) and DNA damage (DNA)) in marine mussels (Mytilus spp.) from a known pristine hybrid zone. Levels of all biomarker expression varied between seasons and appeared to be linked to the reproductive cycle. Oxidative stress in winter, with low GST expression and a higher expression of LPO and DNA damage displayed could be explained by low food availability. These data provide vital baseline information for future ecotoxicological and environmental monitoring studies.     

PAH phototoxicity--an ecologically irrelevant phenomenon?

Photoenhanced toxicity of polycyclic aromatic hydrocarbons (PAH) is well demonstrated in laboratory and in a few in situ studies. Effects have been observed for multiple taxa and toxicological endpoints, and the mechanism of toxic action has been described. However, this phenomenon is ameliorated by physical, chemical and biotic factors. The ecological relevance of PAH phototoxicity remains uncertain; it should not be used for environmental management decisions unless its ecological relevance is firmly established, and then only as part of a weight of evidence determination.     

Seasonal and spatial variation in lipid and triacylglycerol levels in juvenile chinook salmon (Oncorhynchus tshawytscha) from the Bridge River, British Columbia

Triacylglycerols (TAGs) are the primary form of energy storage in fish, but little work has been done on the dynamics of TAG storage and use in relation to environmental conditions. We sampled age-0 chinook salmon (Oncorhynchus tshawytscha) in two reaches of a regulated river in British Columbia, Canada that had different discharge regimes. During the summer, fish from the reach with high freshet flows grew more slowly and had lower TAG levels than those from the reach with lower and more stable flows. In addition, smaller individuals had lower TAG levels than larger ones. We suggest that in the reach with higher flows fish were unable to obtain sufficient surplus energy for somatic growth and lipid storage. In the fall, when flows were lower, TAG storage increased and the proportion of total lipids that were TAGs were similar for both small and large fish. The allocation of energy to TAG stores was likely a strategy to ensure individuals had sufficient energy for overwintering. Our results suggest that individual-based variation in TAG levels may be sensitive to environmental factors and can be used as a measure of fish condition and performance, but more work is needed to fully understand lipid dynamics in seasonally and spatially variable rearing environments.     

Prediction of bioconcentration and related lethal and sublethal effects with aquatic organisms

It is now well established that the octanol/water partition coefficient (K_0W) can be used to estimate bioconcentration of persistent organic compounds, such as the chlorohydrocarbons as well as PAHs and other hydrophobic substances. However, while these relationships are well established in the laboratory, use in the field often poses a number of problems. In recent studies of contaminants in fish from Australia, bioconcentration has been described using additional information on specimen size, lipid content and fish movement patterns.The use of internal biotic concentration provides an additional new and different perspective on toxicant behaviour as compared to the conventional ambient aqueous concentration-based toxicity measures. The internal lethal concentration for persistent organic compounds approaches a constant value for many compounds, and at these concentrations lethal effects are observed. This constant internal lethal concentration provides a basis for predicting toxicity and its relationship to exposure period. In addition, sublethal effects can be successfully related to the internal biotic concentration.     

Physical constraints affecting bacterial habitats and activity in unsaturated porous media – a review

The immense diversity of microbial life found in the vadose zone reflects the extremely heterogeneous and highly dynamic aquatic and chemical environments formed within soil pore spaces. The notion of planktonian free swimming microbes is unrealistic under most unsaturated conditions. Experimental and theoretical evidence suggests that surface attachment is the prevailing lifestyle, where bacterial colonies are embedded in biosynthesized extracellular polymeric substances (EPS). This strategy represents a successful adaptation to the variable and unpredictable hydration conditions near the earth surface. The EPS matrix serves as the interface with the environment; it enhances hydration and transport properties in the immediate vicinity of microbial cells, and dampens effects of highly transient fluctuations in water and nutrient fluxes. The primary effect of soil pore geometry and hydration status is on diffusion pathways to and away from stationary microbial colonies. Microbial dependency on diffusion processes occurs at all scales, but is particularly important at the colony scale. We illustrate the critical role of diffusion pathways with their complex spatial and temporal patterns in promoting coexistence and diversity. We review specific features and adaptations of microbial life to the particular conditions of terrestrial soil environments. The physical and related chemical conditions that shape microbial habitats and govern key processes in unsaturated soils are reviewed in a quantitative framework. Key physiological adaptations and biological responses to challenges presented by unsaturated conditions are discussed. Finally, we discuss potential impacts of microbial activity on properties and characteristics of the host porous medium. This review is an attempt to establish an interdisciplinary dialogue between hydrologists and microbiologists towards a quantitative integration of the role of hydrologic conditions on microbial activity and the role of microbiology in controlling macroscopic fluxes within this important compartment of the biosphere.     

Bioaccumulation of organochlorinated contaminants in three estuarine fish species (Mullus barbatus,Mugil cephalus and Dicentrarcus labrax)

The bioaccumulation of organochlorinated contaminants (DDTs, PCBs and HCB) in three representative fish species from the Ebro Delta (western Mediterranean) was studied. The species, red mullet (Mullus barbatus), sea mullet (Mugil cephalus) and sea bass (Dicentrarchus labrax), were selected for their characteristic habitats and feeding behaviours to investigate their potential as bioindicators in pollution monitoring studies. Higher levels of PCBs and DDTs were generally found in red mullet and could be related to the higher lipid content of this species. Red mullet and sea bass exhibited a similar distribution pattern of these pollutants, whereas DDTs and HCB (hexaclorobenzene) were relatively more abundant in sea mullet, probably as a result of a direct uptake from the water lagoons from where the latter were collected and where these pollutants have been found in higher concentrations. A decrease in concentrations with size (age) was generally observed in red mullet and sea bass, though less clearly in sea mullet. This decrease was more pronounced for DDTs, probably owing to metabolic transformations. However, when data were normalized to lipid content, evidence for a positive uptake by sea mullet was obtained, probably relating to the larger growth rate of this species. These results indicate that the accumulation of organochlorine compounds in coastal fish from the same area depends on lipid content, habitat, dietary intake, growth rate and the metabolism of each species. Although these fish can be used for pollution monitoring, the subsequent variability of pollutant body burdens that are influenced by these factors precludes the extrapolation of data from one species to another.     

Small-scale patterns of meiofauna in a bryophyte covered tufa barrier (Plitvice Lakes,Croatia)

Meiobenthic fauna is complex and essential part of the stream benthos and it is known as intermediaries from bacteria to higher trophic levels. However, the dynamics and mechanisms regulating this community at small-scale largely have been neglected. This study was carried out to determine meiofaunal dynamics in a small scale-patterns influenced by flow velocity and other abiotic and biotic factors. We examined meiofauna within bryophytes on a tufa barrier in Plitvice Lakes National Park using a detailed taxonomic approach of various meiofaunal groups and their feeding guilds. We choose three microhabitats (slow, medium, fast) differing significantly in flow velocity above bryophytes. Bdelloid rotifers were the most abundant group in microhabitat with highest flow velocity, while in other two microhabitats nematodes and monogonont rotifers prevailed in abundance. Data on environmental variables and main meiofaunal taxa and feeding guilds were analyzed using redundancy analysis. This analysis indicated that microfilter feeding guild (e.g. bdelloid rotifers) was strongly affected by interaction of flow velocity and POM fractions. Other feeding guilds were influenced by temperature, oxygen and/or pH and did not prefer high flow velocity. Suction-feeder nematodes and microfilter-feeder rotifers were dominant on temporal and spatial scale, indicating their good adaptations on frequently disturbed conditions that prevailed on bryophyte covered tufa barrier. Our results provide comprehensive survey of diversity, density as well as trophic structure of meiofauna in aquatic bryophytes. Differences in meiofaunal composition and density between three microhabitats suggest that the meiofauna is relevant indicator of environmental changes even at small-scale pattern.     

Distinct distribution revealing multiple bacterial sources for 1-Omonoalkyl glycerol ethers in terrestrial and lake environments

The 1-O-monoalkyl glycerol ethers(MAGEs) were initially viewed as the biomarkers for sulfate-reducing bacteria(SRB) mediating anaerobic oxidation of methane in the marine environments. However, limited information is known about their distribution in terrestrial and other aquatic settings including soils, fresh water lakes, and cave sediments, which may obscure our understanding of their biological sources. Here we found that MAGEs were ubiquitous but differed obviously in distributional pattern among those environments. The surface soils are dominated generally by i C15:0-MAGE, followed by n C16:0-MAGE whereas the lake sediments show the opposite, resulting in significantly higher i C15:0/n C16:0 ratios in soils than in lake sediments. The cave deposits are characterized by considerably higher proportions of branched MAGEs than the former two environments. The logarithm of i C15:0/a C15:0 ratio shows a significant negative correlation with soil p H, likely reflecting an adaptation of microbial cell membrane to change in the ambient proton concentration. The MAGE profiles in cultured bacteria cannot fully explain the MAGE distribution in all the samples analyzed. Therefore, MAGEs in soil, lake sediments, and cave deposits likely have additional biological source(s) other than SRB and cultured MAGE-producing bacteria. The difference in MAGE pattern among environments is likely to be attributed to change in microbial communities.