Microbial Material Research Articles

Microbial material cycling, energetic constraints and ecosystem expansion in subsurface ecosystems.

To harvest energy from chemical reactions, microbes engage in diverse catabolic interactions that drive material cycles in the environment. Here, we consider a simple mathematical model for cycling reactions between alternative forms of an element (A and Ae), where reaction 1 converts A to Ae and reaction 2 converts Ae to A. There are two types of microbes: type 1 microbes harness reaction 1, and type 2 microbes harness reaction 2. Each type receives its own catabolic resources from the other type and provides the other type with the by-products as the catabolic resources. Analyses of the model show that each type increases its steady-state abundance in the presence of the other type. The flux of material flow becomes faster in the presence of microbes. By coupling two catabolic reactions, types 1 and 2 can also expand their realized niches through the abundant resource premium, the effect of relative quantities of products and reactants on the available chemical energy, which is especially important for microbes under strong energetic limitations. The plausibility of mutually beneficial interactions is controlled by the available chemical energy (Gibbs energy) of the system. We conclude that mutualistic catabolic interactions can be an important factor that enables microbes in subsurface ecosystems to increase ecosystem productivity and expand the ecosystem.

Approaches for integrating heterogeneous RNA-seq data reveal cross-talk between microbes and genes in asthmatic patients

Sputum induction is a non-invasive method to evaluate the airway environment, particularly for asthma. RNA sequencing (RNA-seq) of sputum samples can be challenging to interpret due to the complex and heterogeneous mixtures of human cells and exogenous (microbial) material. In this study, we develop a pipeline that integrates dimensionality reduction and statistical modeling to grapple with the heterogeneity. LDA(Latent Dirichlet allocation)-link connects microbes to genes using reduced-dimensionality LDA topics. We validate our method with single-cell RNA-seq and microscopy and then apply it to the sputum of asthmatic patients to find known and novel relationships between microbes and genes.

POTENSI CENDAWAN Synnematium sp. SEBAGAI AGENS PENGENDALI Lawana sp. (FLATIDAE; HOMOPTERA)

<p><strong>Potency of Synnematium sp. as biocontrol agent of Lawana sp. (Flatidae; Homoptera)</strong></p><p>Research on potency of Synnematium sp. as biocontrol agent of Lawana sp. was carried out from May to June 2001 with a scries of pathogenicity tests in ield laboratory Narmada (Mataram) and Insect Laboratory Balittro, Bogor. The research consisted of two pats ie: (I) inoculation of the fungi on egg cluster of Lawana sp. of different ages, and (2) inoculation of the fungi with various application methods to the imagoes of Lawana sp.. Results showed that Synnematium sp. could infect 0-4 days old of eggs. Eggs more Uian 4 days old could be also infected, however 3-5% could still hatch to be nymphs. Application to parasitized eggs did not affect the parasitoid to hatch. Tests on the adults showed that 3 days ater inoculation with the fungi, adults of Lawana sp. became weak, while the motality occurred ater 5 days inoculation. Colony of Synnematium sp. on PDA media, primarily was white, then dark small balls sclcrotium, and formed synnemata on the top. The presence of sclerotia and synnemata seemed that the fungi is potential to be developed as microbial insecticide material ("micoinsectiside").</p>

Insight to peroxone-Fe(III) joint conditioning-horizontal electro-dewatering process on water reduction in activated sludge: Performance and mechanisms

Peroxone disintegration–Fe(III) coagulation (peroxone–Fe(III)) joint conditioning was proposed to enhance the horizontal electro-dewatering (HED) effect of activated sludge (AS). Operating parameters were optimized and the evolutions of AS physicochemical properties, water fractions distribution, organic matter, extracellular polymeric substance (EPS) key components, functional groups, and protein secondary structures during the process were identified. Under the optimized joint conditioning parameters, dewatered AS achieved a final water content of 84.88 ± 0.17% and its bound water content (BWC) was decreased by 1.88 ± 0.28 g/g dry solid. During peroxone pretreatment, the yielded HO decreased the AS floc size, disintegrated the EPS network structure and cell wall, released the bound water, and extracted proteins, polysaccharides, and humic acid-like materials. Furthermore, soluble microbial byproduct-like materials (SMBP) in the EPS layers and tyrosine in tightly bound EPS significantly increased. Protein structures were destroyed, decreasing their water affinity. Subsequent Fe(III) addition re-coagulated broken flocs fragments and EPS fractions, built water flow channels, removed tyrosine and SMBP, and reduced α-helix percentage in slime, facilitating AS dewatering. After joint conditioning, the bound water and intracellular substances were further released by HED. Therefore, the peroxone–Fe(III)–HED process exhibited an excellent performance in AS water reduction.

Practical application potential of microbial-phosphorus minerals-alginate immobilized particles on chromium(VI)-bioreduction

Due to the widespread use of chromium (Cr) across various industrial processes, the process of in-situ remediation of Cr-contaminated groundwater has received extensive attention. Previous studies of solid-phase phosphorus sources and microbial immobilization co-strengthening materials have demonstrated that their performance in continuous flow reactions is of great significance towards practical application of these technologies. It was suggested that Microbial-Phosphorus minerals-Alginate (MPA) immobilized particles showed superior performance (high Cr removal efficiency, low phosphorus surplus, and high environmental resistance) in comparisons of non-immobilization systems and different immobilization methods under continuous flow conditions. Microbial community analysis revealed significant differences between different systems as well as between variations in environmental factors, providing further support for the above conclusions. Synthetic wastewater (synthesized by actual groundwater) was also introduced to further verify the practical application potential of MPA immobilized particles. The results of this study provide a new insight and relevant bench scale data to support the enhancement of in-situ Cr(VI) bioremediation.

Study on improving the consolidation properties of microbial cementitious material by promoting spore germination ratio

Abstract Microbial cementitious material, as a new type of green environmental protection cementitious material, was getting more and more attention. In this paper, improving the consolidation properties of microbial cementitious material by promoting spore germination ratio was studied systematically. Evaluation of spore germination was investigated by the absorbance difference between spores and vegetative bodies, and the relationship between absorbance of microbial solution and spore germination ratio was determined. The effect of heat shock, germination agent and nutriment on spore germination was optimized. The results displayed that the suitable heat shock temperature was 70 °C for 10 min, and the optimum germination agent was alanine with 6 mmol/l of concentration, while nutrient could not effectively improve the spore germination ratio. Effect of spore dosage on microstructure and mechanical properties of consolidation sand were also determined. Compared with the control group, consolidation properties of microbial cementitious material with 2.5 g of spores was better, and that with 2.0 g of spores was basically consistent. The results demonstrated that the spore dosage could be reduced after improving the spore germination, and the cost of microbial cementitious material was greatly declined.

Developing Nano-Delivery Systems for Agriculture and Food Applications with Nature-Derived Polymers.

The applications of nanotechnology are wide ranging, and developing functional nanomaterials for agri-food applications from nature-derived polymers is widely conceived as a sustainable approach that is safer for human and animal consumption. In light of this, this review focuses on the advances in the development of nano-delivery systems using nature-derived polymers for agri-food applications. The review opens with a section detailing the different types of nature-derived polymers currently being used in various applications in the agri-food industry with a special mention on microbial extracellular polymeric materials. The major applications of nano-delivery systems in the food sector, such as food fortification and food preservation, as well as in the agricultural sector for controlled release of agrochemicals using nature-derived polymers are discussed. The review ends with a perspective on the safety and public perception of nano-enabled foods with a concluding remark on future directions of incorporating nano-delivery systems for agri-food purposes.

Performance of anaerobic fluidized bed microbial fuel cell with different porous anodes

Abstract Anode materials were used to construct microbial fuel cells (MFCs), and the characteristics of the anodes were important for successful applied performance of the MFCs. Via the cyclic voltammetry (CV) method, the experiments showed that 5 wt% multiwalled carbon nanotubes (MWNTs) were optimal for the PANI/MWNT film anodes prepared using 24 polymerization cycles. The maximum output voltage of the PANI/MWNT film anodes reached 967.7 mV with a power density of 286.63 mW·m−2. Stable output voltages of 860 mV, 850 mV, and 870 mV were achieved when the anaerobic fluidized bed microbial fuel cell (AFBMFC) anodes consisted of carbon cloth with carbon black on one side, copper foam and carbon brushes, respectively. Pretreatment of the anodes before starting the AFBMFC by immersion in a stirred bacterial fluid significantly shortened the AFBMFC startup time. After the AFBMFC was continuously run, the anode surfaces generated active microbial catalytic material.

Metamorphic evolution of carbonate-hosted microbial biosignature

Microbial biosignature assemblages captured within mineral substrates experience extreme pressures (P) and temperatures (T) during rock burial and metamorphism. We subjected natural microbial biofilms hosted within thermal spring carbonate to six high pressure, high temperature (HPHT) conditions spanning 500 and 800 MPa and 200 to 550 °C, to investigate the initial petrographic transformation of organic and inorganic phases. We find biogenic and amorphous silica mineralises increasingly mature organic matter (OM) as temperature and pressure increase, with OM expelled from recrystallised calcite at the highest HPHT, captured within a quartz phase. Sulfur globules associated with microbial filaments persist across all HPHT conditions in association with microbially-derived kerogen. These data demonstrate how microbial material captured within chemically-precipitated sediments petrographically evolves in high grade rocks during their first stages of transformation.

Complexation by Organic Matter Controls Uranium Mobility in Anoxic Sediments.

Uranium contamination threatens the availability of safe and clean drinking water globally. This toxic element occurs both naturally and as a result of mining and ore-processing in alluvial sediments, where it accumulates as tetravalent U [U(IV)], a form once considered largely immobile. Changing hydrologic and geochemical conditions cause U to be released into groundwater. Knowledge of the chemical form(s) of U(IV) is essential to understand the release mechanism, yet the relevant U(IV) species are poorly characterized. There is growing belief that natural organic matter (OM) binds U(IV) and mediates its fate in the subsurface. In this work, we combined nanoscale imaging (nano secondary ion mass spectrometry and scanning transmission X-ray microscopy) with a density-based fractionation approach to physically and microscopically isolate organic and mineral matter from alluvial sediments contaminated with uranium. We identified two populations of U (dominantly +IV) in anoxic sediments. Uranium was retained on OM and adsorbed to particulate organic carbon, comprising both microbial and plant material. Surprisingly, U was also adsorbed to clay minerals and OM-coated clay minerals. The dominance of OM-associated U provides a framework to understand U mobility in the shallow subsurface, and, in particular, emphasizes roles for desorption and colloid formation in its mobilization.

Keberadaan bakteri patogen pada sampel pangan jajanan anak sekolah dasar di Pulau Sapeken, Sumenep, Jawa Timur

School children snacks are food that is found and routinely consumed by children in the school environment.Good and healthy food must be free from hazardous and toxic materials, such as microbial contamination,chemicals and other materials. The consumed food must meet the microbial contamination requirementsbased on SNI (Standar Nasional Indonesia) safety testing. Pathogenic bacteria still a serious problem invarious countries including Indonesia, since they are capable of causing foodborne diseases. Sapeken Islandis located in Sapeken Village, Sapeken District, Sumenep Regency, East Java Province. The purpose of thestudy was to determine the presence of pathogenic bacteria in samples of snacks for school children onSapeken Island. The method used was the Most Probable Number (MPN) for Escherichia coli, Test Numberof Bacillus sp., Test Number of Staphyllococcus sp., Identification of Salmonella, and Total Plate Count(TPC). The test results obtained in the MPN of Escherichia coli included SD M (9.9 ± 3.8) MPN / g, SD 5(8.68 ± 2.73) MPN / g, SD IT (5.08 ± 0.66) MPN / g, and SD 4 (4.26 ± 2.44) MPN / g exceed the SNI limit.JURNAL BIOLOGI UDAYANA 23(2): 60-71 P ISSN: 1410-5292 E ISSN: 2599-285661The results of JPT E. coli in snack empek-empek at SD I and SD 2, and JPT E. coli ojek in all elementaryschools is <3 MPN / g. The results of the empek-empek and ojek samples in all elementary schools for alltests with the parameter number Bacillus sp. is <1 x 103, the number of Staphylococcus sp. is <1 x 102,Salmonella identification is negative, TPC is <1 x 105 CFU / g. The conclusion of the study is snack forschool children (empek-empek) and ojek on Sapeken Island does not contain contamination of pathogenicbacteria Escherichia coli, Bacillus sp., Staphylococcus sp., Salmonella identification, and TPC, except forthe JPT E. coli test on empek empek in SD M, SD 5, SD IT and SD 4 that exceed SNI limits.

The conversion of organic nitrogen by functional bacteria determines the end-result of ammonia in compost

The conversion of organic nitrogen determines the quality of composting and its environmental impact, but its underlying microbial mechanism is unclear. Hence, in static composting reactors with forced ventilation, vegetable waste, straw and pig manure were used as raw materials to simulate the composting for 33 days with or without adding 9% biochar. In composting, amino acid and amino sugar nitrogen were most easily converted to ammonium and hydrolysable unknown nitrogen was synthesized from ammonium. The aprA and chiA-related bacteria converted amino acid nitrogen to ammonium, and ammonium to hydrolysable unknown nitrogen, while amoA and HAO-related bacteria converted amine and amino sugar nitrogen to ammonium. Additionally, soluble microbial byproduct-like materials (62.4%) significantly affect organic nitrogen transformation, and could reduce ammonia emission by increasing ammoxidation rates. Thus, whether or not adsorbent substances are added, microorganisms affect the production of ammonia by controlling the conversion of organic nitrogen.

Perspectives for Consideration in the Development of Microbial Cell Reference Materials.

Microbiome measurement and analyses benefit greatly from incorporation of reference materials as controls. However, there are many points to consider in defining an ideal whole-cell reference material standard. Such a standard would embody all the diversity and measurement challenges present in real samples, would be completely characterized to provide "ground truth" data, and would be inexpensive and widely available. This ideal is, unfortunately, not readily attainable because of the diverse nature of different sequencing projects. Some applications may benefit most from highly complex reference materials, while others will value characterization or low expense more highly. The selection of appropriate microbial whole-cell reference materials to benchmark and validate microbial measurements should be considered carefully and may vary among specific applications. In this article, we describe a perspective on the development of whole-cell microbial reference materials for use in metagenomics analyses.

Experimental study on repair of fractured rock mass by microbial induction technology.

The surrounding rock mass is often required to have good strength and impermeability in underground engineering. Some grouting methods, such as the chemical grouting method and the cement grouting pressure pump method, are often applied to reform underground environment and improve the engineering performance of rock mass. However, the application of some traditional grouting materials would destroy the original environment in which the project is located. This paper focuses on the repairing effect of Bacillus pasteurii composites in fractured rocks. The repairing effect of microbial materials on fractured sandstone is analysed through nuclear magnetic resonance (NMR) and unconfined compression-shearing equipment. The result shows that the longer the repairing time is, the better the effect will be. After 42 days of repairing, the porosity of fractured sandstone decreases by 36.41%, the impermeability increases by 94.62%, and the compressive strength increases by 30.52%. Through the study of reaction mechanisms, this technology has the advantages of mild reaction conditions, no pollution and good environmental compatibility. The application of this technology to the maintenance of geotechnical engineering can provide new ideas for the research and development of new environmental grouting materials and underground space reconstruction technology.

Effect of alkyl polyglycosides on the performance of thermophilic bacteria pretreatment for saline waste sludge hydrolysis

In this study, alkyl polyglycosides (APG) was used to further accelerate the hydrolysis of saline waste sludge with thermophilic bacteria (TB) pretreatment. In the presence of 0.4 g/g TSS APG, the concentrations of soluble chemical oxygen demand (SCOD), soluble carbohydrate and soluble protein in dissolved organic matters (DOM) were 0.4, 2.4 and 1.3 times of that without APG addition, respectively. Excitation emission matrix (EEM) fluorescence spectroscopy revealed that the addition of APG led to the increase of soluble microbial materials and the decrease of fulvic acid-like substances in DOM, which was beneficial for the subsequent process of anaerobic digestion. Using APG promoted the releasing of enzymes trapped in saline waste sludge and improved the activity of enzymes during hydrolysis. The activities of α-glucosidase and protease increased by 8.8% and 21.3% respectively in the presence of 0.4 g/g TSS APG comparing no APG addition.

Public Microbial Resource Centers: Key Hubs for Findable, Accessible, Interoperable, and Reusable (FAIR) Microorganisms and Genetic Materials.

In the context of open science, the availability of research materials is essential for knowledge accumulation and to maximize the impact of scientific research. In microbiology, microbial domain biological resource centers (mBRCs) have long-standing experience in preserving and distributing authenticated microbial strains and genetic materials (e.g., recombinant plasmids and DNA libraries) to support new discoveries and follow-on studies. These culture collections play a central role in the conservation of microbial biodiversity and have expertise in cultivation, characterization, and taxonomy of microorganisms. Information associated with preserved biological resources is recorded in databases and is accessible through online catalogues. Legal expertise developed by mBRCs guarantees end users the traceability and legality of the acquired material, notably with respect to the Nagoya Protocol. However, awareness of the advantages of depositing biological materials in professional repositories remains low, and the necessity of securing strains and genetic resources for future research must be emphasized. This review describes the unique position of mBRCs in microbiology and molecular biology through their history, evolving roles, expertise, services, challenges, and international collaborations. It also calls for an increased deposit of strains and genetic resources, a responsibility shared by scientists, funding agencies, and publishers. Journal policies requesting a deposit during submission of a manuscript represent one of the measures to make more biological materials available to the broader community, hence fully releasing their potential and improving openness and reproducibility in scientific research.

Viral Metagenomics in the Clinical Realm: Lessons Learned from a Swiss-Wide Ring Trial.

Shotgun metagenomics using next generation sequencing (NGS) is a promising technique to analyze both DNA and RNA microbial material from patient samples. Mostly used in a research setting, it is now increasingly being used in the clinical realm as well, notably to support diagnosis of viral infections, thereby calling for quality control and the implementation of ring trials (RT) to benchmark pipelines and ensure comparable results. The Swiss NGS clinical virology community therefore decided to conduct a RT in 2018, in order to benchmark current metagenomic workflows used at Swiss clinical virology laboratories, and thereby contribute to the definition of common best practices. The RT consisted of two parts (increments), in order to disentangle the variability arising from the experimental compared to the bioinformatics parts of the laboratory pipeline. In addition, the RT was also designed to assess the impact of databases compared to bioinformatics algorithms on the final results, by asking participants to perform the bioinformatics analysis with a common database, in addition to using their own in-house database. Five laboratories participated in the RT (seven pipelines were tested). We observed that the algorithms had a stronger impact on the overall performance than the choice of the reference database. Our results also suggest that differences in sample preparation can lead to significant differences in the performance, and that laboratories should aim for at least 5–10 Mio reads per sample and use depth of coverage in addition to other interpretation metrics such as the percent of coverage. Performance was generally lower when increasing the number of viruses per sample. The lessons learned from this pilot study will be useful for the development of larger-scale RTs to serve as regular quality control tests for laboratories performing NGS analyses of viruses in a clinical setting.

Decimeter-scale mapping of carbonate-controlled trace element distribution in Neoarchean cuspate stromatolites

Ancient stromatolites can provide key insights into the early evolution of life on Earth. Neoarchean fenestrate stromatolites from the ∼2520 Ma Upper Nauga Formation (Transvaal Supergroup, South Africa) preserve cuspate morphologies. They possess clearly delineated support and drape structures interpreted as dolomitized microbial mat material. Petrographic observations show that the biogenic structures are composed of planar-s to non-planar ferroan dolomite, encased in ferroan calcite, including herringbone calcite textures. The cuspate stromatolites were analyzed using Synchrotron Rapid Scanning X-Ray Fluorescence (SRS-XRF) and more conventional techniques to determine: (i) whether element distributions could be distinguished in ancient stromatolites at both cm to dm scales, (ii) whether element distributions show variation between biogenic and abiogenic textures, and (iii) the sample’s paragenesis. The distributions of Ca, Fe, Mn, Pb, Cu, As, Br, Al, Si, P, and S directly correspond to dolomitized stromatolitic structures and show trace element distributions are principally controlled by calcite and dolomite occurrence. Dolomite formation was mainly driven by seawater-derived fluids given the high concentrations of Fe and retention of marine shale-normalized rare earth element and yttrium (REY SN ) patterns, however the spatial association of dolomite to stromatolite structures may reflect microbially-influenced mineral nucleation. Given the complexity of this sample’s paragenetic evolution, trace metal distributions cannot be conclusively tied to specific metabolic pathways, bioaccumulation or passive binding, however, the results show SRS-XRF can be used for quantifiable, spatial, in-situ investigation of ancient microbialites.

Apparent nutrient and fatty acid digestibilities of microbial raw materials for rainbow trout (Oncorhynchus mykiss) with comparison to conventional ingredients

Determination of apparent digestibility coefficients (ADC) of ingredients has a central importance in formulation of aquaculture diets. Heterotrophic and phototrophic grown microalgae are considered as one of the best eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA) as well as protein alternatives for fish oil and fish meal (FM) to sustain further growth in aquaculture production. This study aimed to determine nutrient and fatty acid ADCs of microbial materials including Nannochloropsis oceanica, Phaeodactylum tricornutum and two thraustochytrid strains (T29 and T66) with comparison to commonly used ingredients such as two batches of FMs, poultry-by product meal (PBM), soybean meal (SBM), corn gluten meal (CGM), wheat gluten meal (WGM) and whole wheat flour (WF) in rainbow trout, Oncorhynchus mykiss. Each ingredient was tested using Cr2O3 as an indigestible marker in triplicated cylindro-conical tanks for 2 weeks. Protein ADCs of microbial ingredients ranged between 77.6% in T66 and 84.4% in P. tricornutum and were close to those of FMs and PBM. N. oceanica had generally significantly lower lipid and fatty acid ADCs than those of P. tricornutum, thraustochytrids and the conventional feed ingredients probably due to their thick cell walls. Between the thraustochytrids strains, the T66 appeared to have slightly lower lipid, energy, organic matter, saturated, monounsaturated, long chain n-6 and long chain n-3 fatty acid ADCs than T29. P. tricornutum showed comparable nutrient ADC values to the two FMs used in the study. The results suggest that even if the microbial ingredients were used at 30% in reference diet without exposition to a pretreatment process, they can be utilized at acceptable rates by rainbow trout.

Molecular features of organic matter in anthropogenic earthen mounds, canals and lagoons in the Pago Lindo archaeological complex (Tacuarembó, Uruguayan lowlands) are controlled by pedogenetic processes and fire practices

The Pago Lindo site in the River Plate basin (Uruguay) is an important pre-hispanic mound settlement (ca. 3000–600 BP), of which the technologically and socially advanced nature have only recently been revealed. Different angles of pedogenetic and palaeo-ecological science are rapidly improving our understanding of the history of the site and the relationships between human activity and habitat alteration. Here we add to this progress by molecular characterization of soil organic matter (SOM) in anthropogenic earthen mounds, canals and lagoons from Pago Lindo, by pyrolysis-GC–MS. The results showed that the SOM in the earthen mound and the archaeological lagoon are composed of microbial (partially chitin), aliphatic (partially root-derived) and pyrogenic (from fireplaces or wildfires) materials, whereas the canal and younger lagoon contained SOM with larger proportions of relatively intact plant remains (lignin and polysaccharides from herbaceous species). In most systems, a clear degradation trend can be observed with increasing depth –either from intact plant remains to microbial tissues (canal, young lagoon), or from microbial tissues to recalcitrant aliphatic and pyrogenic sources (earthen mound, ancient lagoon)– which is indicative of a strong control of decay intensity on SOM composition. Multivariate statistics confirmed that most variability in pyrolysis fingerprints can be attributed to degradation/preservation dynamics, which probably erased most of the molecular information on habitat development under the influence of past societies, including nearby maize cultivation.