Microorganisms In Biogeochemical Cycling Research Articles

Case study on a coniferous plantation site about inter-annual shifts in microbial communities under short-term detritus input manipulations

Soil microorganisms are key regulators of soil carbon (C) and nutrients cycles in terrestrial ecosystems. However, it remains uncertain how the inter-annual variation in soil microbial community corresponds well with resource availability in the changing environment. Here, we investigated soil microbial community structure and abundance, as well as the associated environmental variables from 2015 to 2017 under different plant detritus input manipulation treatments in a coniferous (Platycladus orientalis (Linn.) Franco) plantation forest ecosystem in subtropical China. Our results showed that the inter-annual variation in soil microbial community was more visible than that caused by detritus input manipulations, owing to the temporal alterations in microclimates and substrate availability. Both aboveground litter removal and root exclusion had more negative effects on the bacterial PLFAs than fungi except half a year after detritus input manipulations. While, soil microbial abundance increased only after three years of litter addition compared to control. Litter removal, especially the no input treatment significantly increased the fungi to bacteria (F:B) and Gram-positive to Gram-negative bacteria (GP:GN) ratios after one and two years of detritus input manipulations. Whereas, the litter addition treatment had minor effects on these parameters. A clear discrimination of microbial community structure among the different detritus input manipulations appeared after two and three years. Both the F:B and GP:GN ratios were positively related to the carbon to nitrogen (C:N) ratio, recalcitrance index of carbon (RIC) and nitrogen (RIN). Overall, our results reveal that the inter-annual variations in soil microbial community are clearly differentiated by the environmental variables and substrate availability that occur in different years and detritus input manipulations. Our results also suggest that due to the vital role of microorganisms in biogeochemical cycling, shifts in the microbial community structure with altered plant detritus input could profoundly affect ecosystem processes in the long run.

Thermodynamically favorable reactions shape the archaeal community affecting bacterial community assembly in oil reservoirs.

Microbial community assembly mechanisms are pivotal for understanding the ecological functions of microorganisms in biogeochemical cycling in Earth's ecosystems, yet rarely investigated in the context of deep terrestrial ecology. Here, the microbial communities in the production waters collected from water injection wells and oil production wells across eight oil reservoirs throughout northern China were determined and analyzed by proportional distribution analysis and null model analysis. A 'core' microbiota consisting of three bacterial genera, including Arcobacter, Pseudomonas and Acinetobacter, and eight archaeal genera, including Archaeoglobus, Methanobacterium, Methanothermobacter, unclassified Methanobacteriaceae, Methanomethylovorans, Methanoculleus, Methanosaeta and Methanolinea, was found to be present in all production water samples. Canonical correlation analysis reflected that the core archaea were significantly influenced by temperature and reservoir depth, while the core bacteria were affected by the combined impact of the core archaea and environmental factors. Thermodynamic calculations indicate that bioenergetic constraints are the driving force that governs the enrichment of two core archaeal guilds, aceticlastic methanogens versus hydrogenotrophic methanogens, in low- and high-temperature oil reservoirs, respectively. Collectively, our study indicates that microbial community structures in wells of oil reservoirs are structured by the thermodynamic window of opportunity, through which the core archaeal communities are accommodated directly followed by the deterministic recruiting of core bacterial genera, and then the stochastic selection of some other microbial members from local environments. Our study enhances the understanding of the microbial assembly mechanism in deep terrestrial habitats. Meanwhile, our findings will support the development of functional microbiota used for bioremediation and bioaugmentation in microbial enhanced oil recovery.

Microbial weathering signatures in lateritic ferruginous duricrusts

Iron-rich duricrusts (canga) that blanket iron ore deposits in tropical regions in Brazil have a complex formation and evolution. The direct role of microorganisms in the biogeochemical cycling of iron and remarkably aluminium, which is critical for the preservation of these duricrusts, is becoming more apparent. In this study we combine nanoscale secondary ion mass spectrometry (NanoSIMS) with Raman spectroscopy and scanning electron microscopy to distinguish highly weathered and recycled grains, portions of which have been metasomatised by iron in solution, from new mineral precipitates within canga. Microbially-accelerated weathering of grains within canga appears to promote iron, aluminium and titanium oxide mineral dissolution. Anatase forms at the boundaries of rutile grains, highlighting titanium dissolution and re-precipitation at the mineral-scale. Titanium is absent from the authigenic cements in canga. Aqueous ferrous iron, which is sensitive to changes in the oxidation potential of the solution, readily oxidises and re-precipitates in the pore spaces in proximity to preserved microorganisms, leaving aluminium as the most abundant cation in solution. Changes in solution pH and/or organic chemistry causes aluminium to precipitate from solution as gibbsite that infills pore spaces as the final geological texture. Evidence for microbially-promoted weathering includes the fossilisation of microorganisms along grain boundaries, in which aluminium, titanium, chromium and iron are depleted. Immobile elements including titanium, chromium and thorium, associated with rounded fossilised biofilms also indicate that microorganisms have completely weathered grains and become fossilised in place, texturally replacing the grain in the process. Microorganisms also play a role in iron and aluminium precipitation, providing sites for mineral nucleation. These results highlight the microscale changes in oxidation potential, pH and organic chemistry throughout canga that are likely to be influenced by the microbiome and associated flora. Understanding the role of microorganisms in iron biogeochemical cycling will contribute to the accelerated re-cementation of iron-rich duricrusts after the completion of iron ore mining, providing a substrate for revegetation using native plant species. This study also sheds light on direct (microfossils) and indirect (biologically-influenced element mobility) biosignatures in iron-rich geological materials.

Community structure and distribution of benthic Bacteria and Archaea in a stratified coastal lagoon in the Southern Gulf of Mexico

Coastal lagoons are important aquatic systems with strong physicochemical gradients, where the participation of microorganisms in biogeochemical cycles has been well recognised; however, to date, the microbial diversity and distribution in these environments remains under-investigated. Here, three distinguished regions (oligohaline, marine and the mixing) of a transitional coastal lagoon were explored to characterise the structure and composition of benthic microbial communities through 16S rRNA gene Illumina-sequencing, for both Bacteria and Archaea domains. Principal coordinate analysis showed differences in the community structure according to the analysed zones. PERMANOVA analysis evidenced that, of the measured variables, sample zonation and salinity were the main environmental factors explaining the variance of the prokaryotic assemblages. Differentially abundant microbial taxa were detected for each region of the lagoon by LEfSe analysis. Representative members of anaerobic methanogens/methanotrophs (Methanosaetaceae, ANME 1-b and WSA2) were enriched in the oligohaline sediments, while the coastal marine zone had a community represented mainly by Sandaracinaceae, Aminicenantes and Thaumarchaeota (Group-C3). The sediments in the mixing zone had higher abundance of Flavobacteriaceae, Syntrophobacteraceae and uncultured Thermoplasmatales, Bathyarchaeota and Lokiarchaeota. This study expands the available information of the composition and distribution of uncultured Bacteria and Archaea in transitional coastal lagoons, contributing to a systematic understanding of the functioning of these ecosystems.

Detecting metabolic activities in single cells, with emphasis on nanoSIMS

Investigating the contribution of microbial populations to biochemical processes of global significance is challenging as there are few approaches that can detect microbial metabolic activities on single-cell level. Given the widespread distribution and importance of microorganisms in elemental transformations, improved methods for measuring microbial activities in naturally occurring microbial communities is essential. In this article, microautoradiography (MAR), Raman microspectroscopy, and Secondary Ion Mass Spectrometry (SIMS) and their combination with isotope labeling and molecular genetic methods for cell identification (i.e. FISH and related methods) are reviewed. We focus our review on the application of MAR-FISH, Raman-FISH, and FISH-SIMS to environmental samples, with a more detailed description of the use of nanoSIMS-based methodologies to identify, quantify, and visualize the incorporation of labeled substrates of single microorganisms in complex microbial communities. We highlight examples from the marine habitat. In addition, relevant technical aspects as well as important considerations concerning sample preparation and handling are presented. We conclude with a perspective on the usefulness of such tools to study the role of microorganisms in biogeochemical cycling from micron to global scales.

Geobiological investigations using secondary ion mass spectrometry: microanalysis of extant and paleo‐microbial processes

The application of secondary ion mass spectrometry (SIMS) has tremendous value for the field of geobiology, representing a powerful tool for identifying the specific role of micro-organisms in biogeochemical cycles. In this review, we highlight a number of diverse applications for SIMS and nanoSIMS in geobiological research. SIMS performs isotope and elemental analysis at microscale enabling the investigation of the physiology of individual microbes within complex communities. Additionally, through the study of isotopic or chemical characteristics that are common in both living and ancient microbial communities, SIMS allows for direct comparisons of potential biosignatures derived from extant microbial cells and their fossil equivalents.

The role of micro‐organisms in the ecological connectivity of running waters

Summary1. Riparian zones hold a central place in the hydrological cycle, owing to the prevalence of surface and groundwater interactions. In riparian transition zones, the quality of exfiltrating water is heavily influenced by microbial activities within the bed sediments. This paper reviews the role of micro‐organisms in biogeochemical cycling in the riparian‐hyporheic ecotone.2. The production of organic substances, such as cellulose and lignin, by riparian vegetation is an important factor influencing the pathways of microbial processing in the riparian zone. For example, anaerobic sediment patches, created by entrainment of allochthonous organic matter, are focal sites of microbial denitrification.3. The biophysical structure of the riparian zone largely influences in‐stream microbial transformations through the retention of organic matter. Particulate and dissolved organic matter (POM and DOM) is retained effectively in the hyporheic zone, which drives biofilm development and associated microbial activity.4. The structure of the riparian zone, the mechanisms of POM retention, the hydrological linkages to the stream and the intensity of key biogeochemical processes vary greatly along the river continuum and in relation to the geomorphic setting. However, the present state of knowledge of organic matter metabolism in the hyporheic zone suggests that lateral ecological connectivity is a basic attribute of lotic ecosystems.5. Due to their efficiency in transforming POM into heterotrophic microbial biomass, attached biofilms form an abundant food resource for an array of predators and grazers in the interstitial environments of rivers and streams. The interstitial microbial loop, and the intensity of microbial production within the bed sediments, may be a primary driver of the celebrated high productivity and biodiversity of the riparian zone.6. New molecular methods based on the analysis of the low molecular weight RNA (LMW RNA) allow unprecedented insights into the community structure of natural bacterial assemblages and also allow identification and study of specific strains hitherto largely unknown.7. Research is needed on the development and evaluation of sampling methods for interstitial micro‐organisms, on the characterization of biofilm structure, on the analysis of the biodegradable matter in the riparian‐hyporheic ecotone, on the regulation mechanisms exerted on microbiota by interstitial predators and grazers, and on measures of microbial respiration and other key activities that influence biogeochemical cycles in running waters.8. Past experiences from large‐scale alterations of riparian zones by humans, such as the River Rhine in central Europe, undeniably demonstrate the detrimental consequences of disconnecting rivers from their riparian zones. A river management approach that uses the natural services of micro‐organisms within intact riparian zones could substantially reduce the costs of clean, sustainable water supplies for humans.

The Insoluble Problems of Crime

Preface. Preface to the First Edition. Preface to the Second Edition. PART A. FUNDAMENTALS OF MICROBIOLOGY. 1. The Microbial World. 2. Microbial Metabolism and Growth. 3. Role of Microorganisms in Biogeochemical Cycles. PART B. PUBLIC HEALTH MICROBIOLOGY. 4. Pathogens and Parasites in Domestic Wastewater. 5. Microbial Indicators of Fecal Contamination. 6. Water and Wastewater Disinfection. PART C. MICROBIOLOGY OF WASTEWATER TREATMENT. 7. Introduction to Wastewater Treatment. 8. Activated Sludge Process. 9. Bulking and Foaming in Activated Sludge Plants. 10. Processes Based on Attached Microbial Growth. 11. Waste Stabilizations Ponds. 12. Sludge Microbiology. 13. Anaerobic Digestion of Wastewater and Biosolids. 14. Bioaerosols and Bioodors from Wastewater Treatment Plants. PART D. MICROBIOLOGY OF DRINKING WATER TREATMENT. 15. Microbiological Aspects of Drinking Water Treatment. 16. Microbiological Aspects if Drinking Water Distribution. 17. Bioterrorism and Drinking Water Safety. PART E. BIOTECHNOLOGY IN WASTEWATER TREATMENT. 18. Pollution Control Biotechnology. PART F. FATE AND TOXICITY OF CHEMICALS IN WASTEWATER TREATMENT PLANTS. 19. Fate of Xenobiotics and Toxic Metals in Wastewater Treatment Plants. 20. Toxicity Testing in Wastewater Treatment Plants Using Microorganisms. PART G. MICROBIOLOGY AND PUBLIC HEALTH ASPECTS OF WASTEWATER EFFLUENTS AND BIOSOLIDS DISPOSAL AND REUSE. 21. Public Health Aspects of Wastewater and Biosolids Disposal on Land. 22. Public Health Aspects of Wastewater and Biosolids Disposal in the Marine Environment. 23. Wastewater Reuse. References. Index.