Dissimilar bacterial and fungal decomposer communities across rich to poor fen peatlands exhibit functional redundancy

2015 ◽  
Vol 95 (3) ◽  
pp. 219-230 ◽  
Author(s):  
Kristine M. Haynes ◽  
Michael D. Preston ◽  
James W. McLaughlin ◽  
Kara Webster ◽  
Nathan Basiliko
Keyword(s):  
Organic Matter ◽  
Microbial Communities ◽  
Environmental Changes ◽  
Functional Redundancy ◽  
Organic Substrates ◽  
Metabolic Potential ◽  
Vegetation Communities ◽  
Chemical Complexity ◽  
Poor Fen

Haynes, K. M., Preston, M. D., McLaughlin, J. W., Webster, K. and Basiliko, N. 2015. Dissimilar bacterial and fungal decomposer communities across rich to poor fen peatlands exhibit functional redundancy. Can. J. Soil Sci. 95: 219–230. Climatic and environmental changes can lead to shifts in the dominant vegetation communities present in northern peatland ecosystems, including from Sphagnum- to vascular-dominated systems. Such shifts in vegetation result in changes to the chemical quality of carbon substrates for soil microbial decomposers, with leaves and roots deposited in the peat surface and subsurface that potentially decompose faster. This study characterized the bacterial and fungal communities present along a nutrient gradient ranging from rich to poor fen peatlands and assessed the metabolic potential of these communities to mineralize a variety of organic matter substrates of varying chemical complexity using substrate-induced respiration (SIR) assays. Distinct microbial communities existed between rich, intermediate and poor fens, but SIR in each of the three sites exhibited the same pattern of carbon mineralization, providing support for the concept of functional redundancy, at least under standardized in vitro conditions. Preferential mineralization of simple organic substrates in the rich fen and complex compounds in the poor fen was not observed. Similarly, no preference was given to “native” organic matter extracts derived from each fen, with microbial communities opting for the most bioavailable substrate. This study suggests that soil bacteria and fungi might be able to respond relatively rapidly to shifts in vegetation communities and subsequent changes in the quality of carbon substrate additions to peatlands associated with environmental and climatic change.

scholarly journals Deciphering the functioning of microbial communities: shedding light on the critical steps in metaproteomics

2019 ◽  
Author(s):  
Augustin Géron ◽  
Johannes Werner ◽  
Ruddy Wattiez ◽  
Philippe Lebaron ◽  
Sabine Matallana-Surget
Keyword(s):  
Microbial Communities ◽  
Protein Identification ◽  
Environmental Changes ◽  
Rapid Development ◽  
Complex Structure ◽  
Molecular Tools ◽  
Protein Functions ◽  
The Impact ◽  
And Oxidative Stress

AbstractUnraveling the complex structure and functioning of microbial communities is essential to accurately predict the impact of perturbations and/or environmental changes. From all molecular tools available today to resolve the dynamics of microbial communities, metaproteomics stands out, allowing the establishment of phenotype-genotype linkages. Despite its rapid development, this technology has faced many technical challenges that still hamper its potential power. How to maximize the number of protein identification, improve quality of protein annotation and provide reliable ecological interpretation, are questions of immediate urgency. In our study, we used a robust metaproteomic workflow combining two protein fractionation approaches (gel-based versus gel-free) and four protein search databases derived from the same metagenome to analyze the same seawater sample. The resulting eight metaproteomes provided different outcomes in terms of (i) total protein numbers, (ii) taxonomic structures, and (iii) protein functions. The characterization and/or representativeness of numerous proteins from ecologically relevant taxa such as Pelagibacterales, Rhodobacterales and Synechococcales, as well as crucial environmental processes, such as nutrient uptake, nitrogen assimilation, light harvesting and oxidative stress response were found to be particularly affected by the methodology. Our results provide clear evidences that the use of different protein search databases significantly alters the biological conclusions in both gel-free and gel-based approaches. Our findings emphasize the importance of diversifying the experimental workflow for a comprehensive metaproteomic study.

Clearer than mud? Using environmental DNA to track historical shifts in lake communities.

2021 ◽  
Author(s):  
John Pearman ◽  
Laura Biessy ◽  
Georgia Thomson-Laing ◽  
Lizette Reyes ◽  
Claire Shepherd ◽  
...  
Keyword(s):  
New Zealand ◽  
Microbial Communities ◽  
Environmental History ◽  
Environmental Changes ◽  
Environmental Dna ◽  
Taxonomic Composition ◽  
Molecular Methods ◽  
Rrna Gene ◽  
Metabolic Potential ◽  
Dna And Rna

<p>A continuous record of environmental history is stored in lake sediments providing an avenue to explore current and historical lake communities. Traditionally paleolimnological methods have focussed on macroscopic indicators (e.g. pollen, chronomids, diatoms) to investigate environmental changes but the application of environmental DNA techniques has enabled the investigation of microbial communities and other soft bodied organisms through time. The ‘Our lakes’ health; past, present, future (Lakes380)’ project aims to combined traditional and molecular methods to explore shifts in biological communities over the last 1,000 years (pre-human arrival in New Zealand). Sediments cores have been collected from a wide diversity of lakes across New Zealand and 16S rRNA gene metabarcoding approaches of both DNA and RNA applied to reveal how microbial community changes across time and especially in response to the arrival of humans and associated changes to the landscape and lake environments. We further investigate the changes in inferred metabolic potential of the microbial communities as the taxonomic composition of the lake differs over time. Finally, we combine these novel molecular methods with hyperspectral scanning and pollen data to increase the knowledge of changes in lake communities and identifying the timing of changes in lake health. The combination of methodologies provides a greater understanding of the environmental history of lake systems and will help to inform management decisions relating to the restoration and protection of lake health.</p>

scholarly journals Off-site impacts of agricultural composting: role of terrestrially derived organic matter in structuring aquatic microbial communities and their metabolic potential

2014 ◽  
Vol 90 (3) ◽  
pp. 622-632 ◽  
Author(s):  
Thomas Pommier ◽  
Asmaa Merroune ◽  
Yvan Bettarel ◽  
Patrice Got ◽  
Jean-Louis Janeau ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Communities ◽  
Metabolic Potential

scholarly journals Metabolic profiling suggests two sources of organic matter shape microbial activity, but not community composition, in New Zealand fjords

2019 ◽  
Author(s):  
Sven P. Tobias-Hünefeldt ◽  
Stephen R. Wing ◽  
Federico Baltar ◽  
Sergio E. Morales
Keyword(s):  
Organic Matter ◽  
Microbial Communities ◽  
Microbial Activity ◽  
Community Composition ◽  
Sediment Resuspension ◽  
Metabolic Diversity ◽  
New Production ◽  
Metabolic Potential ◽  
Microbial Carbon ◽  
And Function

AbstractFjords are semi-enclosed marine systems with unique physical conditions that influence microbial communities structure. Pronounced organic matter and physical condition gradients within fjords provide a natural laboratory for the study of changes in microbial phylogeny and metabolic potential in response to environmental conditions (e.g. depth). In the open ocean new production from photosynthesis supplies organic matter to deeper aphotic layers, sustaining microbial activity. We measured the metabolic diversity and activity of microbial communities in fjords to determine patterns in metabolic potential across and within fjords, and whether these patterns could be explained by community composition modifications. We demonstrated that metabolic potential and activity are shaped by similar parameters as total (prokaryotic and eukaryotic) microbial communities. However, we identified increases in metabolic diversity and potential (but not in community composition) at near bottom (aphotic) sites consistent with the influence of sediments in deeper waters. Thus, while composition and function of the microbial community in the upper water column was likely shaped by marine snow and sinking POM generated by new production, deeper sites were strongly influenced by sediment resuspension of benthic organic matter generated from this or other sources (terrestrial, chemoautotrophic, microbial carbon loop), uncoupling the community composition and function dynamics.

scholarly journals Influence of taxonomic and functional content of microbial communities on the quality of fermented cocoa pulp-bean mass

2021 ◽  
Author(s):  
Jatziri Mota-Gutierrez ◽  
Ilario Ferrocino ◽  
Manuela Giordano ◽  
Mirna Leonor Suarez-Quiroz ◽  
Oscar Gonzalez-Ríos ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Microbiological Quality ◽  
Chemical Properties ◽  
Metabolic Potential ◽  
Shotgun Metagenomics ◽  
Fermentation Time ◽  
Physico Chemical ◽  
The Difference ◽  
The Impact

The microbial metabolism drives the changes in the physico-chemical properties and consequently the sensory characteristics of fermented cocoa beans. In this context, information regarding the structure, function and metabolic potential of microbial communities’ present during cocoa pulp-bean mass fermentation is limited, especially concerning the formation of aromatic compounds. To bridge the gap, the metagenome of fermented cocoa pulp-bean mass (Criollo and Forastero) has been investigated using shotgun metagenomics coupled with physico-chemical, microbiological, quality and sensory analysis to explore the impact of microbial communities on the quality of fermented cocoa pulp-bean mass on one farm in one season and in one region under the same environmental conditions. Our findings showed that the metagenomic diversity in cocoa, fermentation length, and the diversity and function of metagenome-assembled genomes (MAGs) greatly influence the resulting distinctive flavours. From the metabolic perspective, multiple indicators suggest that the heterolactic metabolism was more dominant in Criollo fermentations. KEGG genes were linked with the biosynthesis of acetic acid, ethanol, lactic acid, acetoin and phenylacetaldehyde during Criollo and Forastero fermentations. MAGs belonging to Lactiplantibacillus plantarum, Limosilactobacillus reuteri and Acetobacter pasteurianus were the most prevalent. The fermentation time and roasting are the most important determinants of cocoa quality while the difference between the two varieties are relatively minor. The assessment of microbiological and chemical analysis is an urgent need for developing fermentation protocols according to regions, countries and cocoa varieties to guarantee safety and desirable flavour development. Importance. Monitoring the composition, structure, functionalities and metabolic potential encoded at the level of DNA of fermented cocoa pulp-bean mass metagenome is of great importance for food safety and quality implications.

scholarly journals All-In-One: Microbial Response to Natural and Anthropogenic Forcings in a Coastal Mediterranean Ecosystem, the Syracuse Bay (Ionian Sea, Italy)

2021 ◽  
Vol 10 (1) ◽  
pp. 19
Author(s):  
Gabriella Caruso ◽  
Maria Grazia Giacobbe ◽  
Filippo Azzaro ◽  
Franco Decembrini ◽  
Marcella Leonardi ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Community ◽  
Community Dynamics ◽  
Heterotrophic Bacteria ◽  
Nutrient Concentrations ◽  
Mediterranean Ecosystem ◽  
Organic Substrates ◽  
Metabolic Potential ◽  
Microbial Response ◽  
Phytoplankton Communities

Bacterial and phytoplankton communities are known to be in close relationships, but how natural and anthropogenic stressors can affect their dynamics is not fully understood. To study the response of microbial communities to environmental and human-induced perturbations, phytoplankton and bacterial communities were seasonally monitored in a Mediterranean coastal ecosystem, Syracuse Bay, where multiple conflicts co-exist. Quali-quantitative, seasonal surveys of the phytoplankton communities (diatoms, dinoflagellates and other taxa), the potential microbial enzymatic activity rates (leucine aminopeptidase, beta-glucosidase and alkaline phosphatase) and heterotrophic culturable bacterial abundance, together with the thermohaline structure and trophic status in terms of nutrient concentrations, phytoplankton biomass (as Chlorophyll-a), and total suspended and particulate organic matter, were carried out. The aim was to integrate microbial community dynamics in the context of the environmental characterization and disentangle microbial patterns related to natural changes from those driven by the anthropic impact on this ecosystem. In spite of the complex relationships between the habitat characteristics, microbial community abundance and metabolic potential, in Syracuse Bay, the availability of organic substrates differently originated by the local conditions appeared to drive the distribution and activity of microbial assemblage. A seasonal pattern of microbial abundances was observed, with the highest concentrations of phytoplankton in spring and low values in winter, whereas heterotrophic bacteria were more abundant during the autumn period. The autumn peaks of the rates of enzymatic activities suggested that not only phytoplankton-derived but also allochthonous organic polymers strongly stimulated microbial metabolism. Increased microbial response in terms of abundance and metabolic activities was detected especially at the sites directly affected by organic matter inputs related to agriculture or aquaculture activities. Nitrogen salts such as nitrate, rather than orthophosphate, were primary drivers of phytoplankton growth. This study also provides insights on the different seasonal scenarios of water quality in Syracuse Bay, which could be helpful for management plans of this Mediterranean coastal environment.

scholarly journals The quality of dissolved organic matter shapes the biogeography of the active bathypelagic microbiome

2021 ◽  
Author(s):  
Marta Sebastian ◽  
Pablo Sanchez ◽  
Guillem Salazar ◽  
Xose A Alvarez-Salgado ◽  
Isabel Reche ◽  
...  
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Environmental Changes ◽  
Large Fraction ◽  
Free Living ◽  
Lower Growth ◽  
Differential Abundance ◽  
Differential Abundance Analysis

The bathypelagic ocean (1000-4000 m depth) is the largest aquatic biome on Earth but it is still largely unexplored. Due to its prevalent low dissolved organic carbon concentrations, most of the prokaryotic metabolic activity is assumed to be associated to particles. The role of free-living prokaryotes has thus been mostly ignored, except that of some chemolithoautotrophic lineages. Here we used a global bathypelagic survey of size-fractionated metagenomic and 16S (genes and transcripts) data and performed a differential abundance analysis to explore the functional traits of the different prokaryotic life-strategies, their contribution to the active microbiome, and the role that the quality of the dissolved organic matter (DOM) plays in driving this contribution. We found that free-living prokaryotes have limited capacity to uplift their metabolism in response to environmental changes and display comparatively lower growth rates than particle associated prokaryotes, but are responsible for the synthesis of vitamins in the bathypelagic. Furthermore, their contribution to the active prokaryotic microbiome increased towards waters depleted of labile DOM, which represented a large fraction of the tropical and subtropical ocean sampled stations. This points to a relevant yet overlooked role of free-living prokaryotes in DOM cycling in the vast bathypelagic desert.

Spatial distribution of sediment archaeal and bacterial communities relates to the source of organic matter and hypoxia – a biogeographical study on Lake Remoray (France)

2021 ◽  
Author(s):  
Vincent Tardy ◽  
David Etienne ◽  
Hélène Masclaux ◽  
Valentin Essert ◽  
Laurent Millet ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Geostatistical Approach ◽  
Water Layers ◽  
Trophic Network ◽  
Bottom Waters ◽  
Abundance Variation ◽  
Microbial Groups

Abstract Bottom waters hypoxia spreads in many lakes worldwide causing severe consequences on whole lakes trophic network. Here, we aimed at understanding the origin of organic matter stored in the sediment compartment and the related diversity of sediment microbial communities in a lake with deoxygenated deep water layers. We used a geostatistical approach to map and compare both the variation of organic matter and microbial communities in sediment. Spatialisation of C/N ratio and δ13C signature of sediment organic matter suggested that Lake Remoray was characterized by an algal overproduction which could be related to an excess of nutrient due to the close lake-watershed connectivity. Three spatial patterns were observed for sediment microbial communities after the hypoxic event, each characterized by specific genetic structure, microbial diversity and composition. The relative abundance variation of dominant microbial groups across Lake Remoray such as Cyanobacteria, Gammaproteobacteria, Deltaproteobacteria and Chloroflexi provided us important information on the lake areas where hypoxia occurs. The presence of methanogenic species in the deeper part of the lake suggests important methane production during hypoxia period. Taken together, our results provide an extensive picture of microbial communities' distribution related to quantity and quality of organic matter in a seasonally hypoxic lake.

scholarly journals A Comparison of Two-Stage and Traditional Co-Composting of Green Waste and Food Waste Amended with Phosphate Rock and Sawdust

2021 ◽  
Vol 13 (3) ◽  
pp. 1109
Author(s):  
Edgar Ricardo Oviedo-Ocaña ◽  
Angélica María Hernández-Gómez ◽  
Marcos Ríos ◽  
Anauribeth Portela ◽  
Viviana Sánchez-Torres ◽  
...  
Keyword(s):  
Organic Matter ◽  
Product Quality ◽  
Food Waste ◽  
Phosphate Rock ◽  
Pilot Scale ◽  
Two Stage ◽  
Green Waste ◽  
Wet Weight ◽  
Two Phases

The composting of green waste (GW) proceeds slowly due to the presence of slowly degradable compounds in that substrate. The introduction of amendments and bulking materials can improve organic matter degradation and end-product quality. However, additional strategies such as two-stage composting, can deal with the slow degradation of green waste. This paper evaluates the effect of two-stage composting on the process and end-product quality of the co-composting of green waste and food waste amended with sawdust and phosphate rock. A pilot-scale study was developed using two treatments (in triplicate each), one being a two-stage composting and the other being a traditional composting. The two treatments used the same mixture (wet weight): 46% green waste, 19% unprocessed food waste, 18% processed food waste, 13% sawdust, and 4% phosphate rock. The traditional composting observed a higher degradation rate of organic matter during the mesophilic and thermophilic phases and observed thermophilic temperatures were maintained for longer periods during these two phases compared to two-stage composting (i.e., six days). Nonetheless, during the cooling and maturation phases, the two treatments had similar behaviors with regard to temperature, pH, and electrical conductivity, and the end-products resulting from both treatments did not statistically differ. Therefore, from this study, it is concluded that other additional complementary strategies must be evaluated to further improve GW composting.

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