Microbial traces and their role in forensic science

Forensic microbiology, also known as the microbiology of death, is an emerging branch of science that is still underused in criminal investigations. Some of the cases might be difficult to solve with commonly used forensic methods, and then they become an operational field for microbiological and mycological analyses. The aim of our review is to present significant achievements of selected studies on the thanatomicrobiome (micro-organisms found in the body, organs and fluids after death) and epinecrotic community (micro-organisms found on decaying corpses) that can be used in forensic sciences. Research carried out as a part of the forensic microbiology deals with the thanatomicrobiome and the necrobiome—communities of micro-organisms that live inside and outside of a putrefying corpse. Change of species composition observed in each community is a valuable feature that gives a lot of information related to the crime. It is mainly used in the estimation of post-mortem interval (PMI). In some criminal investigations, such noticeable changes in the microbiome and mycobiome can determine the cause or the actual place of death. The microbial traces found at the crime scene can also provide clear evidence of guilt. Nowadays, identification of micro-organisms isolated from the body or environment is based on metagenome analysis and 16S rRNA gene amplicon-based sequencing for bacteria and ITS rRNA gene amplicon-based sequencing for fungi. Cultivation methods are still in use and seem to be more accurate; however, they require much more time to achieve a final result, which is an unwanted feature in any criminal investigation.     

Leaf litter decomposition characteristics and controlling factors across two contrasting forest types

两种不同森林类型叶凋落物分解特征及影响因子研究 叶凋落物分解为森林生态系统提供了重要的能量和养分来源。除传统的环境因素外,叶凋落物的降解过程也受到绿叶功能性状和叶凋落物基质质量的影响。然而,在群落水平上,绿叶功能性状和叶凋落物基质质量对不同森林群落叶凋落物分解的相对重要性仍不清楚。因此,本研究以北京东灵山地区7种典型森林群落类型的混合叶凋落物为研究对象,利用分解袋法通过360天的野外相似环境分解实验对叶凋落物的分解过程进行了研究。这些森林群落包括6种分别以胡桃楸(Juglans mandshurica)、青杨(Populus cathayana)、棘皮桦(Betula dahurica)、白桦(Betula platyphylla)、油松(Pinus tabuliformis) 和华北落叶松(Larix gmelinii var. principis-rupprechtii) 为优势种的单优种群落,以及一种以大叶白蜡(Fraxinus rhynchophylla)、蒙古栎(Quercus mongolica)和蒙椴(Tilia mongolica)为优势种的共优种群落。研究结果表明,不同森林群落之间叶凋落物分解速率存在显著差异。群落聚合的植物功能性状和叶凋落物基质质量分别解释了群落叶凋落物分解速率变异的35.60%和9.05%,两者交互作用解释率为23.37%,表明群落聚合的植物功能性状及其与叶凋落物基质质量的共同作用是影响群落叶凋落物分解速率变异的主要因素。通过冗余分析发现,叶片氮含量、叶干物质含量、叶片单宁含量和比叶面积能显著影响群落叶凋落物分解速率的变异。因此,在对群落水平上叶凋落物分解的研究应该关注群落聚合的绿叶功能性状对分解的影响。     

A stable alpha-helix-rich intermediate is formed by a single mutation of the beta-sheet protein, src SH3, at pH 3

Recently, we have found a transient intermediate on the folding pathway of src SH3. Intending to investigate the structure of the transient intermediate, we tested a mutant of src SH3, named A45G, using circular dichroism, fluorescence and X-ray solution scattering, and incidentally found that it forms a stable alpha-helix-rich intermediate (I(eq)) (different from the native beta-sheet-based secondary structure) at pH 3.0, but contains only beta-sheets at pH 6.0, whereas wild-type SH3 forms only beta-sheets at both pH 3.0 and pH 6.0. The intermediate I(eq) shows a circular dichroism measured at theta(222)=-10,300 deg.cm(2) dmol(-1), indicating a 31% alpha-helix proportion, as estimated by the CONTIN program. X-ray scattering gave the radius of gyration for I(eq) as 19.1 A at pH 3.0 and 15.4 A at pH 6.0, and Kratky plots showed a clear peak at pH 3.0, 4.0 and 6.0, indicating that I(eq) too is compact. In these parameters, I(eq) closely resembles the kinetically-obtained intermediate I(kin) which we found on the folding pathway of wild-type SH3 at pH 3.0 (radius of gyration 18.7 A and theta(222)=-8700 deg.cm(2)dmol(-1)), indicating a 26% alpha-helix proportion in our previous paper. Refolding experiments with A45G were done at pH 6.0 by stopped-flow apparatus monitored by circular dichroism, and compared to kinetic experiments with wild-type SH3 at pH 6.0. The result showed an alpha-helix-rich intermediate at the same dichroism amplitude, but nine times slower in formation-rate. A pH-jump experiment from pH 3.0 to pH 5.9 on A45G was also performed. This showed no bursts, and the rate of conformation-change was almost as fast as the refolding rate of A45G at pH 6.0. These kinetic experiment data would be consistent with I(eq) being nearly identical to the I(kin), which appeared on the folding pathways of both wild-type SH3 and A45G at pH 3.     

耕作方式对绿洲灌区农田土壤有机碳及其分布的影响

依托自2005年开始的田间定位试验,分析了传统平作(CT)、垄作沟灌(FRB)、固定道垄作(PRB)和固定道平作(ZT)4种耕作方式下绿洲灌区农田0～90 cm土层中土壤总有机碳(TOC)、颗粒态有机碳(POC)含量和微生物生物量碳(SMBC)及其分布特征.结果表明: 4种耕作方式下土壤TOC、POC和SMBC在土壤剖面中的垂直分布特征相似,有机碳含量随着土层深度的增加而递减,且处理之间差异逐渐减小.PRB可显著提高TOC、POC含量和SMBC,不同耕作方式下各土层有机碳含量表现为PRB>ZT>FRB>CT.与CT相比,0～10 cm土层中PRB、ZT和FRB处理TOC含量分别增加11.1%～24.8%、9.1%～18.7%和7.8%～8.2%,POC含量分别增加24.1%～26.5%、17.3%～18.7%和-8.2%～10.8%,SMBC分别增加20.5%～28.3%、10.4%～15.2%和3.5%～3.7%.TOC对POC具有明显促进作用.PRB能显著增加土壤POC分配比例,增加有机碳积累.     

Integrating plant litter quality,soil organic matter stabilization,and the carbon saturation concept

Labile, ‘high‐quality’, plant litters are hypothesized to promote soil organic matter (SOM) stabilization in mineral soil fractions that are physicochemically protected from rapid mineralization. However, the effect of litter quality on SOM stabilization is inconsistent. High‐quality litters, characterized by high N concentrations, low C/N ratios, and low phenol/lignin concentrations, are not consistently stabilized in SOM with greater efficiency than ‘low‐quality’ litters characterized by low N concentrations, high C/N ratios, and high phenol/lignin concentrations. Here, we attempt to resolve these inconsistent results by developing a new conceptual model that links litter quality to the soil C saturation concept. Our model builds on the Microbial Efficiency‐Matrix Stabilization framework (Cotrufo et al., 2013) by suggesting the effect of litter quality on SOM stabilization is modulated by the extent of soil C saturation such that high‐quality litters are not always stabilized in SOM with greater efficiency than low‐quality litters.     

Muscular strength and power are correlated with motor unit action potential amplitudes,but not myosin heavy chain isoforms in sedentary males and females

It remains unclear if the sizes of higher-threshold motor units (MU) are associated with muscular strength and power. Therefore, the purpose of this study was to examine sex-related differences in muscle cross-sectional area (mCSA), percent myosin heavy chain (%MHC) isoform expression, and the MU action potential amplitudes (MUAP_AMPS)-recruitment threshold (RT) relationships of the vastus lateralis and isometric peak torque, isokinetic peak torque and mean power at 1.05 rad·s⁻¹ of the leg extensors. Surface electromyographic decomposition techniques were used to quantify MUAP_AMPS recorded during isometric muscle actions at 70% of maximal voluntary contractions and regressed against RTs with the slopes calculated. Ultrasound images were used to measure mCSA. Males had greater slopes from the MUAP_AMP-RT relationship than the females (P < 0.05). The greater slopes likely reflected larger higher-threshold MUs for the males. The mCSAs and slopes from the relationships were strongly correlated with isometric and isokinetic peak torque and isokinetic mean power (r = 0.78–0.82), however, type I %MHC isoform was only moderately correlated with isometric peak torque (r = −0.54). The results indicated that sex-related differences in muscular strength and power were associated more so with the sizes of the higher-threshold MUs (slopes) and mCSA than MHC isoforms. The amount of cross-bridge activity within muscle fibers that comprise higher-threshold MUs may be the primary contributor to muscular strength and power rather than the contractile properties of the muscle.     

Structural and functional aspects of treated mine water and aquaculture effluent streams

Multiple effluent streams may flow into a single receiving stream making it difficult to understand the effects of a single effluent source or the interactions between effluents. In this study, we examined benthic community structure and function in an effluent stream formed by the release of treated mine water, in treated mine water that had been used as a water source for flow-through aquaculture and below the confluence of the two. This study demonstrated that macroinvertebrate communities, while taxonomically simple, developed in treated mine water. The addition of aquaculture effluent to the treated mine water allowed colonization by additional taxa, increased leaf decomposition rates and may have conferred resistance to a turbidity event. Ecosystem responses were mediated by the surrounding terrestrial environment. In shaded conditions macroinvertebrate densities could be as much as 10× higher and the taxa were dominated by simuliids and chironomids, while in open conditions filamentous algae flourished and the taxa were dominated by hydroptilids and chironomids. Consequently, consideration of stream processes that promote preferred ecological processes, such as macroinvertebrate production and organic matter processing, when siting effluent streams may reduce impacts on receiving streams.     

Analysis of the bacterial community developing in the course of <Emphasis Type="Italic">Sphagnum</Emphasis> moss decomposition

Slow degradation of organic matter in acidic Sphagnum peat bogs suggests a limited activity of organotrophic microorganisms. Monitoring of the Sphagnum debris decomposition in a laboratory simulation experiment showed that this process was accompanied by a shift in the water color to brownish due to accumulation of humic substances and by the development of a specific bacterial community with a density of 2.4 × 10⁷ cells ml^?1. About half of these organisms are metabolically active and detectable with rRNA-specific oligonucleotide probes. Molecular identification of the components of this microbial community showed the numerical dominance of bacteria affiliated with the phyla Alphaproteobacteria, Actinobacteria, and Planctomycetes. The population sizes of the Firmicutes and Bacteroidetes, which are believed to be the main agents of bacterially-mediated decomposition in eutrophic wetlands, were low. The numbers of planctomycetes increased at the final stage of Sphagnum decomposition. The representative isolates of the Alphaproteobacteria were able to utilize galacturonic acid, the only low-molecular-weight organic compound detected in the water samples; the representatives of the Planctomycetes were able to decompose some heteropolysaccharides, which points to the possible functional role of these groups of microorganisms in the community under study. Thus, the composition of the bacterial community responsible for Sphagnum decomposition in acidic and low-mineral oligotrophic conditions seems to be fundamentally different from that of the bacterial community which decomposes plant debris in eutrophic ecosystems at neutral pH.     

玉米秸秆生物炭对秸秆腐熟进程、养分含量和CO2排放量的影响

生物炭具有良好的理化特性(富碳、呈碱性、孔隙丰富),能够有效调节其所在系统的理化性质.通过室内培养试验研究了玉米秸秆生物炭对玉米秸秆腐熟进程以及腐熟产物的理化性质、养分含量和CO₂气体排放的影响.试验设置4个处理:对照(CK);生物炭添加量5%(B₁,生物炭干基质量占玉米秸秆腐熟体系的干基质量分数);生物炭添加量10%(B₂);生物炭添加量20%(B₃).结果表明: 生物炭能够提高秸秆腐熟体系的升温速率和温度峰值,加快秸秆腐熟进程;生物炭能够提高秸秆腐熟过程中微生物活跃时期的pH值,提高秸秆腐熟体系的电导率(EC),为微生物降解有机物提供更适宜的环境;生物炭能够促进秸秆腐熟体系有机质的降解,增加秸秆腐熟体系的总养分含量,提高秸秆腐熟产物的品质.另外,随着生物炭添加量的提高,氮(N)含量没有显著变化,磷(P₂O₅)含量和钾(K₂O)含量都显著提高.其中,B₃处理的P₂O₅和K₂O含量较CK分别提高了0.2%和0.9%.生物炭添加能够提高秸秆腐熟体系CO₂的排放通量,且CO₂排放通量与温度的变化趋势一致,进一步说明生物炭能够提高微生物降解有机物的强度.