Role of specific microbial communities in the bioavailability of iron in Doñana National Park

The Doñana National Park contains highly complex microbial communities that play critical roles in the bioavailability and biogeochemical cycling of elements. In this study, we analyzed the formation of Fe-rich films on the surface of shallow waters at Doñana National Park as a model for future applications in bioremediation. Phytoplankton composition and abundance, physicochemical measurements, culture enrichments, and molecular detection of microorganisms were determined during this study. Natural samples were incubated in the laboratory and enrichments producing similar phenomena were obtained. Bacteria belonging to the genera Enterobacter were the major participants in surface Fe-film formation in laboratory enrichments. Film formation was dependent on wind exposure and only those sites protected from the direct influence of wind developed these films. A higher concentration of euglenophytes was found in the proximity of film-covered waters. Available iron (Fe²⁺) and total Fe concentrations were high (18.8 and 46.6 mg/L, respectively) underneath the surface film, and higher than in film-free waters and pore-sediment water. The concentration of phosphate and its availability were higher in the iron-rich film sediment, as 61% of total P was bound to iron oxy-hydroxides. Our results provide evidence of the link between P and Fe biogeochemical cycling in aquatic systems on sandy soils at the Doñana National Park. In addition, they provide significant insights into the bioavailability of these elements with potential interest in the role of microorganisms for metal sequestration in natural environments and utilization in bioremediation processes.     

Collembola gut passage shapes microbial communities in faecal pellets but not viability of dietary algal cells

Microarthropods are known as vectors for soil microorganisms, predominantly fungi. This laboratory study uses the widespread unicellular green algae Chlorella vulgaris as model to assess the role of Collembola in algal dispersal and to determine the effects of gut passage on propagation. Living algal cells were observed in 70 % of the faecal pellets of Folsomia candida, Heteromurus nitidus and Protaphorura fimata. Moreover, marker fatty acids for green algae, i.e. 16:2ω6,9 and 16:3ω3,6,9, were consistently detected in the pellets. Compared to the algal diet, the high content of methyl-branched total lipid fatty acid (TLFA) with hydroxyl substitution indicated microbial colonisation during gut passage. The TLFA profile of faeces revealed no species-specific differences but similar changes in microbial communities over the duration of feeding, indicating comparable indigenous bacteria and colonisation mechanisms during gut passage. In sum, faecal pellets of soil microarthropods such as Collembola can act as a vector for both dietary algae and specific gut-associated microorganisms, with the latter likely involved in resource degradation inside and outside the gut habitat.     

海洋微生物来源的天然产物开发研究进展

综述了近年来海洋微生物来源天然产物研究的新进展,总结了该类天然产物的开发策略.通过对样品采用不同的预处理方式、不同的分离培养基以及新的培养方法,讨论如何获得海洋来源的特有微生物和增加海洋来源微生物类群的多样性.阐述了在海洋微生物天然产物的开发过程中,采用宏基因组技术及基因组测序等手段,来发现难培养或不可培养微生物中的天然产物以及处于"沉默"状态的天然产物.最后介绍了异源生物合成、组合生物合成以及核糖体工程等技术在海洋微生物天然产物开发和改造中的应用,并举例论述了海洋微生物天然产物的开发.     

铁循环微生物对环境中重金属的影响研究进展

铁循环微生物包括铁氧化菌(Fe(Ⅱ)-oxidizing bacteria,FeOB)和铁还原菌(Fe(Ⅲ)-reducing bacteria,FeRB),在由它们介导Fe²⁺(Fe³⁺)氧化(还原)的过程中,往往也伴随着一系列重金属元素的迁移转化,对重金属在环境中的生物有效性和迁移性方面有重要作用.本文综述了环境中的铁循环微生物,针对铁循环微生物驱动重金属迁移转化的作用机制,分别从铁氧化菌氧化亚铁生成铁矿物对重金属的固定,铁还原菌介导铁矿物还原溶解及次生矿物生成,以及铁循环微生物代谢耦合重金属形态转化方面进行阐述;进一步通过研究实例综述了铁循环微生物对环境中砷、镉、铬、铜、铅等重金属的作用及修复潜力;未来的研究可关注特定微生物的成矿机制,生物成矿对重金属固定的调控,以及重金属复合污染场地的铁循环微生物修复应用等方面.本文以期为基于铁循环微生物的重金属污染修复提供理论指导和应用依据.     

大气颗粒物中微生物分析方法及分布特征的研究进展

大气颗粒物(particulate matter, PM)可能携带病原微生物,会对人体健康产生影响,因此,对大气颗粒物中微生物的采集和分析已成为当今的研究热点。本文对大气颗粒物中微生物的采集方法和分析方法(培养法、菌群多样性组成谱测序和宏基因组学技术)的研究进展进行简要概括,着重介绍不同条件下(区域、时间、粒径、天气条件和气象因素)大气颗粒物中微生物的分布状况差异,并对引起相关差异的原因进行了探讨,旨在为深入认识大气颗粒物中微生物的分布特征提供参考。     

Mapping the niche space of soil microorganisms using taxonomy and traits

The biodiversity of microbial communities has important implications for the stability and functioning of ecosystem processes. Yet, very little is known about the environmental factors that define the microbial niche and how this influences the composition and activity of microbial communities. In this study, we derived niche parameters from physiological response curves that quantified microbial respiration for a diverse collection of soil bacteria and fungi along a soil moisture gradient. On average, soil microorganisms had relatively dry optima (0.3 MPa) and were capable of respiring under low water potentials (-2.0 MPa). Within their limits of activity, microorganisms exhibited a wide range of responses, suggesting that some taxa may be able to coexist by partitioning the moisture niche axis. For example, we identified dry-adapted generalists that tolerated a broad range of water potentials, along with wet-adapted specialists with metabolism restricted to less-negative water potentials. These contrasting ecological strategies had a phylogenetic signal at a coarse taxonomic level (phylum), suggesting that the moisture niche of soil microorganisms is highly conserved. In addition, variation in microbial responses along the moisture gradient was linked to the distribution of several functional traits. In particular, strains that were capable of producing biofilms had drier moisture optima and wider niche breadths. However, biofilm production appeared to come at a cost that was reflected in a prolonged lag time prior to exponential growth, suggesting that there is a trade-off associated with traits that allow microorganisms to contend with moisture stress. Together, we have identified functional groups of microorganisms that will help predict the structure and functioning of microbial communities under contrasting soil moisture regimes.     

Discovery of novel halogenase genes using sequence-driven metagenomics approach北大核心CSCD

It is of great significance to ability to obtain new natural products with diverse activities through the study of soil microorganisms. However, less than 1% of the total soil microorganisms can be cultured under laboratory conditions, thus limiting the discovery of new compounds. Metagenomics, by which the genomic DNA of soil microorganisms can be extracted and expressed in heterologous hosts, provides a new approach for the functional study of soil microorganisms. Natural halides have good bioactivities, including antibacterial and antitumor activities. Halogenases play an important role in biosynthesis, and introducing bioactivities of halogenated compounds. To investigate the potential of halogenated compounds production from soil microorganisms, a soil metagenomic library was screened by PCR for clones harboring reduced flavin adenine dinucleotide (FADH2) - dependent halogenase genes. Sixty-five positive clones were identified from the library, and the amino acid sequences of halogenase genes within the positive clones were analyzed. Phylogenetic analyses revealed that more than 85% of these genes were separated from known halogenases to form new clades in the phylogenetic tree; moreover the soilderived halogenases showed high diversity. By further biosynthetic gene analysis of the positive clones, a new type I polyketide biosynthetic gene sequence was identified, which is probably related to the biosynthesis of the halogenated type I polyketide. In conclusion, novel and diverse halogenase genes were identified on sixty-five metagenomic clones using a sequence-driven metagenomic approach, laying a foundation for the further discovery of novel natural halides biosynthetic gene clusters and halides. © 2018 Science Press. All rights reserved.     

Incorporating dormancy in dynamic microbial community models

Biogeochemical activity in natural and engineered systems depends on the abundances, functional capabilities and physiological states of the indigenous microorganisms. Typically, only a fraction of the microbial population is active at any given time. As environmental conditions change, previously active microorganisms may switch to an inactive or dormant state, while dormant ones may become active. Here, we present an extended modeling concept for the growth and decay of microorganisms that explicitly accounts for their ability to switch between active and dormant states. The equations describing the switching between physiological states are implemented into a biogeochemical reaction simulator. The model was used to reproduce published data from two laboratory experiments in which microorganisms were subjected to intermittent substrate supply or reactivated after a prolonged period of starvation. Parameter values obtained from the simulation of these experiments were used for subsequent sensitivity analyses and for the simulation of hypothetical scenarios. Results for hypothetical microbial communities consisting of two competing species exposed to periodic feeding imply that, under certain conditions, an effective dormancy-reactivation strategy may have a competitive advantage over a fast growth strategy. That is, organisms that can switch rapidly in response to fluctuations in external conditions may outcompete fast-growing organisms. Furthermore, certain combinations of growth and dormancy strategies may lead to the long-term coexistence of the two competing species. Overall, the simulated population dynamics show that dormancy is an important feature of microbial communities, which can lead to complex responses to environmental fluctuations.     

亚热带赤红壤不同林型对土壤微生物区系的影响

研究不同人工林型下上壤微生物区系的差异与变化．定期采样测定结果表明，不同林型下的土壤微生物总数顺序为混交林＞豆科纯林＞纯桉林；其数量在一年中随季节变化很大，各种林型均以秋季最大．其次是春、冬季，夏季最小；三大类随中又以细菌所占比例最大，其次为放线菌、真菌；它们各自的优势种群在组成上各林地间差别不大，而且全年都保持较稳定的比例．无论是微生物种类还是其数量，都以混交林多于纯林，而在纯林中又以豆科纯林多于桉林．     

Diversity and distribution of proteorhodopsin-containing microorganisms in marine environments

Proteorhodopsin (PR) is a recently discovered protein involved in the utilization of light energy. Several studies have shown that PR-containing microorganisms are widespread and compose a large proportion of the biomass in marine ecosystems. A better understanding of the ecological role of PR will help clarify the effect of the global flow of energy and the carbon cycle on marine communities. In this study, a bioinformatical database of PR codon sequences, the Global Distribution Database of Proteorhodopsin (GDDP), as a tool for analyzing the diversity and distribution of PR-containing microorganisms in marine environments throughout the world was designed. The community structure of PR microorganisms were also compared using PCR assays and UniFrac analyses of 12 samples collected from three water layers (0, 75, and 200 m) at four representative sites in the Pacific, Atlantic, and Indian Oceans. The results indicate that PRcontaining microorganisms can be grouped into two distribution types: widespread and location-specific. Representative cases of the former include SAR11-PR and HOT2C01-PR. Interestingly, PR communities cluster by geographic locale but not by water depth.     

不同放牧梯度下草甸草原土壤微生物和酶活性研究

通过小区控制放牧实验,研究呼伦贝尔草甸草原不同放牧强度下草地土壤微生物和酶活性的变化。结果表明：不同处理土壤微生物数量表现为细菌〉放线菌〉真菌。不同土层土壤微生物总数不放牧处理大于放牧处理,0～30 cm土层土壤微生物生物量碳、氮含量在轻牧区较高,在中牧区较低。土壤脲酶和过氧化氢酶活性轻度放牧和中度放牧高于不放牧和重度放牧。土壤微生物数量、生物量、土壤蛋白酶和过氧化氢酶活性均随土壤深度的增加呈递减趋势。相关分析表明,土壤微生物数量、微生物生物量以及土壤酶活性相互之间密切相关,土壤微生物量N与细菌达到极显著正相关（P〈0.01）,与真菌和放线菌呈显著相关（P〈0.05）。土壤微生物量C与真菌达到极显著负相关（P〈0.01）,与放线菌呈显著负相关（P〈0.05）。土壤微生物数量、土壤微生物量N与转化酶、蛋白酶、过氧化氢酶活性呈显著或极显著正相关。土壤微生物量C与转化酶、蛋白酶、过氧化氢酶呈显著负相关（P〈0.05）。     

不同陈化烟叶叶面高温微生物多样性

以国内外不同品种、不同陈化时间的10个烟叶样品为材料,对其叶面高温微生物进行了分离纯化、鉴定和多样性研究,以了解表面高温微生物在烟叶陈化发酵中的作用.结果表明:陈化烟叶表面高温菌总量为103~105个/g,高温细菌占绝对优势,真菌很少,未能分离到放线菌和酵母菌;高温细菌主要包括芽孢杆菌属(Bacillus)和地芽孢杆菌属(Geobacillus)两个属,芽孢杆菌属为优势菌属;高温霉菌主要包括青霉属(Penicillium)和曲霉属(Aspergillus),曲霉属为优势菌属.国内外烟叶表面微生物种类和数量有所差异,与陈化时间和烟叶品种等因素有着密切关系.     

肠道微生物受环境污染的影响及其对宿主疾病的调控作用

宿主肠道内存在的大量微生物与其健康状况直接相关,这些微生物是人和动物健康成长不可或缺的。肠道微生物通过多种途径调节人体生理功能的同时也受到人体内外环境的影响。因此,分析建立肠道微生物、相关疾病的产生原因和作用机制以及环境影响因子之间的联系具有重要意义。本文首先针对肠道微生物对人体的物质与能量代谢、先天和获得性免疫、胃肠道功能等方面的影响进行综述。然后重点分析了近年来有关肠道微生物对环境污染所致健康效应的影响及作用机制的研究进展。以期加深肠道微生物与人类健康之间相互作用机理的理解,并为环境毒理学与肠道微生物之间关系的研究提供新的思路。     

Microbial relationships in surface-mine revegetation

The establishment and interrelationships of microorganisms with soil and plant processes during reclamation are greatly influenced by the composition of the planting medium and vegetation practices. While in some instances the parent material may be used as the vegetation medium, the practice of topsoiling, particularly the direct haul method, may be beneficial in introducing microorganisms and improving the quality of the plant growth medium of spoils that are chemically or physically less desirable than the native soils. The influence of different vegetation types on soil development on surface mines may be a reflection of physioiogical differences that affect microbial development in the rhizosphere. Such differences include levels of carbohydrate translocated to the root system and/or released into the surrounding soil; the plant's effectiveness as a mycorrhizal host; and the rate of degradation of plant residues. It has become apparent that microbial interactions are an important part of plant and soil processes in reclamation. While some of the microorganisms important in plant growth and soil development can be introduced readily by management practices, the majority usually are disseminated by natural means and only gradually become a part of the microbial population. More research is needed on developing new methods or refining current procedures for early introduction of these microorganisms in reclamation practices.     

Bacteria inactivation by sulfate radical: progress and non-negligible disinfection by-products

● Status of inactivation of pathogenic microorganisms by SO₄^•− is reviewed. ● Mechanism of SO₄^•− disinfection is outlined. ● Possible generation of DBPs during disinfection using SO₄^•− is discussed. ● Possible problems and challenges of using SO₄^•− for disinfection are presented. Sulfate radicals have been increasingly used for the pathogen inactivation due to their strong redox ability and high selectivity for electron-rich species in the last decade. The application of sulfate radicals in water disinfection has become a very promising technology. However, there is currently a lack of reviews of sulfate radicals inactivated pathogenic microorganisms. At the same time, less attention has been paid to disinfection by-products produced by the use of sulfate radicals to inactivate microorganisms. This paper begins with a brief overview of sulfate radicals’ properties. Then, the progress in water disinfection by sulfate radicals is summarized. The mechanism and inactivation kinetics of inactivating microorganisms are briefly described. After that, the disinfection by-products produced by reactions of sulfate radicals with chlorine, bromine, iodide ions and organic halogens in water are also discussed. In response to these possible challenges, this article concludes with some specific solutions and future research directions.     

Microbial relationships in surface-mine revegetation

The establishment and interrelationships of microorganisms with soil and plant processes during reclamation are greatly influenced by the composition of the planting medium and vegetation practices. While in some instances the parent material may be used as the vegetation medium, the practice of topsoiling, particularly the direct haul method, may be beneficial in introducing microorganisms and improving the quality of the plant growth medium of spoils that are chemically or physically less desirable than the native soils. The influence of different vegetation types on soil development on surface mines may be a reflection of physioiogical differences that affect microbial development in the rhizosphere. Such differences include levels of carbohydrate translocated to the root system and/or released into the surrounding soil; the plant's effectiveness as a mycorrhizal host; and the rate of degradation of plant residues. It has become apparent that microbial interactions are an important part of plant and soil processes in reclamation. While some of the microorganisms important in plant growth and soil development can be introduced readily by management practices, the majority usually are disseminated by natural means and only gradually become a part of the microbial population. More research is needed on developing new methods or refining current procedures for early introduction of these microorganisms in reclamation practices.     

Inactivation and risk control of pathogenic microorganisms in municipal sludge treatment: A review

• Diversity and detection methods of pathogenic microorganisms in sludge. • Control performance of sludge treatment processes on pathogenic microorganisms. • Risk of pathogen exposure in sludge treatment and land application. The rapid global spread of coronavirus disease 2019 (COVID-19) has promoted concern over human pathogens and their significant threats to public health security. The monitoring and control of human pathogens in public sanitation and health facilities are of great importance. Excessive sludge is an inevitable byproduct of sewage that contains human and animal feces in wastewater treatment plants (WWTPs). It is an important sink of different pollutants and pathogens, and the proper treatment and disposal of sludge are important to minimize potential risks to the environment and public health. However, there is a lack of comprehensive analysis of the diversity, exposure risks, assessment methods and inactivation techniques of pathogenic microorganisms in sludge. Based on this consideration, this review summarizes the control performance of pathogenic microorganisms such as enterovirus, Salmonella spp., and Escherichia coli by different sludge treatment technologies, including composting, anaerobic digestion, aerobic digestion, and microwave irradiation, and the mechanisms of pathogenic microorganism inactivation in sludge treatment processes are discussed. Additionally, this study reviews the diversity, detection methods, and exposure risks of pathogenic microorganisms in sludge. This review advances the quantitative assessment of pathogenic microorganism risks involved in sludge reuse and is practically valuable to optimize the treatment and disposal of sludge for pathogenic microorganism control.     

嗜酸微生物生态学与矿物生物浸出技术

综述了嗜酸微生物存在的环境、生态结构和微生物多样性,以及温度、氧对嗜酸微生物的影响.总结了嗜酸微生物群落间存在竞争、捕食、共生、合作等相互作用关系,这对理解矿物的生物浸出具有重要意义.目前对嗜酸微生物生态学的理解主要基于传统的纯菌培养分离技术,但是分子生物学技术的发展提供了更科学的研究手段,将纯菌培养分离技术和分子生物学技术相结合是研究嗜酸微生物生态的有效方法.认为理解嗜酸微生物生态学规律,将有利于开发新的微生物矿物加工技术,我国有必要加强浸矿微生物生态学的研究.表1参24     

Advances in airborne microorganisms detection using biosensors: A critical review

• Airborne microorganism detection methods are summarized. • Biosensors play an important role in detecting airborne microorganisms. • The principle of biosensor detection of airborne microorganisms is introduced. • The application and progress of biosensor in recent years is summarized. • The future perspectives of biosensor are identified. Humanity has been facing the threat of a variety of infectious diseases. Airborne microorganisms can cause airborne infectious diseases, which spread rapidly and extensively, causing huge losses to human society on a global scale. In recent years, the detection technology for airborne microorganisms has developed rapidly; it can be roughly divided into biochemical, immune, and molecular technologies. However, these technologies still have some shortcomings; they are time-consuming and have low sensitivity and poor stability. Most of them need to be used in the ideal environment of a laboratory, which limits their applications. A biosensor is a device that converts biological signals into detectable signals. As an interdisciplinary field, biosensors have successfully introduced a variety of technologies for bio-detection. Given their fast analysis speed, high sensitivity, good portability, strong specificity, and low cost, biosensors have been widely used in environmental monitoring, medical research, food and agricultural safety, military medicine and other fields. In recent years, the performance of biosensors has greatly improved, becoming a promising technology for airborne microorganism detection. This review introduces the detection principle of biosensors from the three aspects of component identification, energy conversion principle, and signal amplification. It also summarizes its research and application in airborne microorganism detection. The new progress and future development trend of the biosensor detection of airborne microorganisms are analyzed.     

Microbes to clean indoor pollutants

Formaldehyde is a dangerous indoor pollutant which is introduced in house by common objects such as furniture. Effective microorganisms have the very interesting ability to degrade some pollutants. Here, we tested the removal of formaldehyde and aromatic aldehydes using effective microorganisms including yeast, lactic acid bacteria, and photosynthetic bacteria. Formaldehyde was quantified by GC–MS of formaldehyde dinitrophenylhydrazone. Other aldehydes were analyzed by GC–MS. Results show that effective microorganisms remove 70–100 % of formaldehyde, benzaldehyde, and 4-methylbenzaldehyde in about a week. Experiments on chipboard panels indicate the possibility to decrease the amount of formaldehyde emission by furniture. This is the first report on the removal of formaldehyde by effective microorganisms, to our best knowledge.