scholarly journals Highly diverse fungal communities in carbon-rich aquifers of two contrasting lakes in Northeast Germany

2019 ◽  
Author(s):  
Anita Perkins ◽  
Lars Ganzert ◽  
Keilor Rojas-Jiménez ◽  
Jeremy Fonvielle ◽  
Grant C. Hose ◽  
...  
Keyword(s):  
Organic Matter ◽  
Community Structure ◽  
Rrna Gene ◽  
28S Rrna ◽  
Ecological Role ◽  
Fungal Community Composition ◽  
Ne Germany ◽  
And Function ◽  
Carbon Processing ◽  
Complex Organic

AbstractFungi are an important component of microbial communities and are well known for their ability to degrade refractory, highly polymeric organic matter. In soils and aquatic systems, fungi play an important role in carbon processing, however, their diversity, community structure and function as well as ecological role, particularly in groundwater, are poorly studied. The aim of this study was to examine the fungal community composition, diversity and function of 16 groundwater boreholes located in the vicinity of two lakes in NE Germany that are characterized by contrasting trophic status. The analysis of 28S rRNA gene sequences amplified from the groundwater revealed high fungal diversity and clear differences in community structure between both aquifers. Most sequences were assigned to Ascomycota and Basidiomycota, but members of Chytridiomycota, Cryptomycota, Zygomycota, Blastocladiomycota, Glomeromycota and Neocallmastigomycota were also detected. In addition, 27 species of fungi were successfully isolated from the groundwater wells and tested for their ability to degrade complex organic polymers – the predominant carbon source in the wells. Most isolates showed positive activities for at least one of the tested polymer types, with three strains, belonging to the genera Gibberella, Isaria and Cadophora, being able to degrade all tested substrates. Our results highlight the high diversity of fungi in groundwater, and point to their important ecological role in breaking down highly polymeric organic matter in these isolated microbial habitats.

scholarly journals Press xenobiotic disturbance favors deterministic assembly with a shift in function and structure of bacterial communities in sludge bioreactors

2020 ◽  
Author(s):  
Ezequiel Santillan ◽  
Hari Seshan ◽  
Stefan Wuertz
Keyword(s):  
Community Structure ◽  
Bacterial Communities ◽  
Temporal Dynamics ◽  
Treatment Plant ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Batch Reactors ◽  
Function Structure ◽  
Community Function ◽  
And Function

AbstractDisturbance is thought to affect community assembly mechanisms, which in turn shape community structure and the overall function of the ecosystem. Here, we tested the effect of a continuous (press) xenobiotic disturbance on the function, structure, and assembly of bacterial communities within a wastewater treatment system. Two sets of four-liter sequencing batch reactors were operated in triplicate with and without the addition of 3-chloroaniline for a period of 132 days, following 58 days of acclimation after inoculation with sludge from a full-scale treatment plant. Temporal dynamics of bacterial community structure were derived from 16S rRNA gene amplicon sequencing. Community function, structure and assembly differed between press disturbed and undisturbed reactors. Temporal partitioning of assembly mechanisms via phylogenetic and non-phylogenetic null modelling analysis revealed that deterministic assembly prevailed for disturbed bioreactors, while the role of stochastic assembly was stronger for undisturbed reactors. Our findings are relevant because research spanning various disturbance types, environments and spatiotemporal scales is needed for a comprehensive understanding of the effects of press disturbances on assembly mechanisms, structure, and function of microbial communities.Graphical abstract

scholarly journals Molecular Basis for Substrate Recognition and Catalysis by a Marine Bacterial Laminarinase

2020 ◽  
Vol 86 (23) ◽  
Author(s):  
Jian Yang ◽  
Yuqun Xu ◽  
Takuya Miyakawa ◽  
Lijuan Long ◽  
Masaru Tanokura
Keyword(s):  
Organic Matter ◽  
Extracellular Enzymes ◽  
Heterotrophic Bacteria ◽  
Substrate Binding ◽  
Substrate Recognition ◽  
Transglycosylation Activity ◽  
Bacterial Utilization ◽  
Carbon Processing ◽  
Structural Levels ◽  
Complex Organic

ABSTRACT Laminarin is an abundant algal polysaccharide that serves as carbon storage and fuel to meet the nutrition demands of heterotrophic microbes. Laminarin depolymerization catalyzed by microbial extracellular enzymes initiates remineralization, a key process in ocean biogeochemical cycles. Here, we described a glycoside hydrolase 16 (GH16) family laminarinase from a marine alga-associated Flavobacterium at the biochemical and structural levels. We found that the endolytic enzyme cleaved laminarin with a preference for β-1,3-glycoside linkages and showed transglycosylation activity across a broad range of acceptors. We also solved and compared high-resolution crystal structures of laminarinase in the apo form and in complex with β-1,3-tetrasaccharides, revealing an expanded catalytic cleft formed following substrate binding. Moreover, structure and mutagenesis studies identified multiple specific contacts between the enzyme and glucosyl residues essential for the substrate specificity for β-1,3-glucan. These results provide novel insights into the structural requirements for substrate binding and catalysis of GH16 family laminarinase, enriching our understanding of bacterial utilization of algal laminarin. IMPORTANCE Heterotrophic bacterial communities are key players in marine biogeochemical cycling due to their ability to remineralize organic carbon. Processing of complex organic matter requires heterotrophic bacteria to produce extracellular enzymes with precise specificity to depolymerize substrates to sizes sufficiently small for uptake. Thus, extracellular enzymatic hydrolysis initiates microbe-driven heterotrophic carbon cycling. In this study, based on biochemical and structural analyses, we revealed the depolymerization mechanism of β-1,3-glucan, a carbon reserve in algae, by laminarinase from an alga-associated marine Flavobacterium. The findings provide new insights into the substrate recognition and catalysis of bacterial laminarinase and promote a better understanding of how extracellular enzymes are involved in organic matter cycling.

scholarly journals Hunters or gardeners? Linking community structure and function of trap-associated microbes to the nutrient acquisition strategy of a carnivorous plant

2017 ◽  
Author(s):  
Dagmara Sirová ◽  
Jiří Bárta ◽  
Karel Šimek ◽  
Thomas Posch ◽  
Jiří Pech ◽  
...  
Keyword(s):  
Community Structure ◽  
Nutrient Recycling ◽  
Carnivorous Plant ◽  
Nutrient Acquisition ◽  
Microbial Consortia ◽  
Acquisition Strategies ◽  
Fresh Perspective ◽  
Recycling Potential ◽  
And Function ◽  
Complex Organic

AbstractAll higher eukaryotes live in a relationship with diverse microorganisms which colonize their bodily surfaces; plants are no exception. However, we still lack a satisfactory understanding of how these loosely associated microbiomes with immense diversity and functional potential interact with their hosts or how these interactions shape processes within populations and ecosystems. There is considerable similarity between microbial communities colonizing plant surfaces such as roots, and those of the animal gut. This often overlooked parallel allows us to look at microbial as well as host ecophysiology from a fresh perspective. The traps of carnivorous plants are sophisticated digestive organs and interface environments between the supply and the demand for nutrients. We selected the miniature ecosystem in the traps of aquatic carnivorousUtriculariaplants as our model system. By assessing the trap-associated microbial community structure, diversity, function, as well as the nutrient recycling potential of bacterivory, we gained insight into the nutrient acquisition strategies of theUtriculariahosts. We conclude that trap ecophysiological function is in many aspects highly analogous to that of the herbivore gut and centers around complex microbial consortia, which act synergistically to covert complex organic matter, often of algal origin, into a source of nutrients for the plants.

scholarly journals Organic soil amendment with Spent Mushroom Substrate results in fungal colonisation, alters bacterial-fungal co-occurrence patterns and improves plant productivity

2019 ◽  
Author(s):  
Fabiana S. Paula ◽  
Enrico Tatti ◽  
Camilla Thorn ◽  
Florence Abram ◽  
Jude Wilson ◽  
...  
Keyword(s):  
Organic Matter ◽  
Community Structure ◽  
Soil Amendment ◽  
Organic Matter Content ◽  
Plant Productivity ◽  
Fungal Communities ◽  
Spent Mushroom Substrate ◽  
Soil System ◽  
Occurrence Patterns ◽  
Complex Organic

AbstractIn agricultural systems based on organic fertilisers, the activity of prokaryotes and fungi is essential for degradation of complex substrates and release of nutrients for plant uptake. Understanding the dynamics of microbial communities in these systems is, therefore, desirable for designing successful management strategies aiming to optimise nutrient availability and to improve plant productivity. Of particular interest is how the microbial inoculum provided by an organic substrate persists in the soil and interacts with soil and plant microbiomes, as these processes may affect the long-term benefits of organic amendments. We aimed to investigate how these dynamics occurred in soil treated with stabilised spent mushroom substrate (SMS), a soil amendment rich in nutrients and complex organic matter. We carried out a 14 weeks soil trial to assess the plant growth promoting properties of the SMS and to monitor the successional processes of the resulting SMS-soil communities compared to a mineral amended control. Bacterial and fungal communities were analysed by high-throughput sequencing at both DNA and RNA (cDNA) levels. Using a combination of computational tools, including SourceTracker and Network analysis, we assessed the persistence of SMS-derived taxa in soil, and the changes in co-occurrence patterns and microbial community structure over time. Prokaryotic and fungal communities presented remarkably distinct trajectories following SMS treatment. The soil prokaryotic communities displayed higher levels of resilience to the changes introduced by SMS treatment and rapidly tended toward a soil-like profile, with low persistence of SMS-derived prokaryotes. In contrast, the SMS fungal community had greater success in soil colonisation during the time monitored. SMS treatment promoted an increase in the participation of fungi in the highly connected fraction of the active community, including fungal taxa of SMS origin. We observed the presence of highly connected microbial guilds, composed by fungal and bacterial taxa with reported capabilities of complex organic matter degradation. Many of these taxa were also significantly correlated with the organic matter content and plant yield, suggesting that these highly connected taxa may play key roles not only in the community structure, but also in the plant-soil system under organic fertilisation.

scholarly journals Effects of organic loading rate on reactor performance and archaeal community structure in mesophilic anaerobic digesters treating municipal sewage sludge

2011 ◽  
Vol 29 (11) ◽  
pp. 1117-1123 ◽  
Author(s):  
Eddie Gómez ◽  
Jay Martin ◽  
Frederick C. Michel
Keyword(s):  
Organic Matter ◽  
Community Structure ◽  
Community Dynamics ◽  
Loading Rate ◽  
Archaeal Community ◽  
Full Scale ◽  
Municipal Sewage Sludge ◽  
Organic Loading Rate ◽  
Rrna Gene ◽  
Organic Loading

In this study, the organic loading rate (OLR) of a high-solids anaerobic digestion (HSAD) system was increased from 3.4 to 5.0 gVS L−1 day−1 and reactor stability, performance and microbial community structure were determined. Laboratory simulations (3.5 L) of the full-scale process (500 dry ton year−1) were conducted using continuously stirred-tank mesophilic reactors. OLRs of 3.4 gVS L−1day−1 (equal to the full-scale HSAD), 4.0, 4.5 and 5.0 gVS L−1day−1 were evaluated. Biochemical parameters and archaeal community dynamics were measured over 42 days of steady state operation. Results showed that increasing OLR increased the amount of organic matter conversion and resulted in higher organic matter removal and volumetric methane (CH4) production (VMP) rates. The highest volatile solids (VS) removal and VMP results of 54 ± 2% and 1.4 ± 0.1 L CH4 L−1day−1 were observed for 5.0 gVS L−1 day−1. The efficiency of reactor conversion of organic matter to CH4 was found to be similar in all the treatments with an average value of 0.57 ± 0.07 LCH4 gVS−1removed. 16S rRNA gene terminal restriction fragment polymorphism (T-RFLP) analyses revealed that archaeal TRFs remained stable during the experiment accounting for an average relative abundance (RA) of 81 ± 1%. Archaea consistent with multiple terminal restriction fragments (TRFs) included members of the Euryarchaeota and Crenarchaeota phyla, including acetoclastic and hydrogenotrophic groups. In conclusion, this laboratory-scale study suggests that performance and stability as well as the archaeal community structure in this HSAD system was unaffected by increasing the OLR by nearly 50% and that this increase resulted in a similar increase in the amount of CH4 gas generated.

scholarly journals Organic matter from Arctic sea-ice loss alters bacterial community structure and function

2019 ◽  
Vol 9 (2) ◽  
pp. 170-176 ◽  
Author(s):  
Graham J. C. Underwood ◽  
Christine Michel ◽  
Guillaume Meisterhans ◽  
Andrea Niemi ◽  
Claude Belzile ◽  
...  
Keyword(s):  
Organic Matter ◽  
Community Structure ◽  
Bacterial Community ◽  
Sea Ice ◽  
Bacterial Community Structure ◽  
Structure And Function ◽  
Arctic Sea Ice ◽  
Arctic Sea ◽  
And Function ◽  
Arctic Sea Ice Loss

scholarly journals Fungal Diversity in Permafrost and Tallgrass Prairie Soils under Experimental Warming Conditions

2013 ◽  
Vol 79 (22) ◽  
pp. 7063-7072 ◽  
Author(s):  
C. Ryan Penton ◽  
Derek StLouis ◽  
James R. Cole ◽  
Yiqi Luo ◽  
Liyou Wu ◽  
...  
Keyword(s):  
Community Structure ◽  
Tallgrass Prairie ◽  
Soil Fungi ◽  
Rrna Gene ◽  
28S Rrna ◽  
Ribosomal Database Project ◽  
Data Set ◽  
Prairie Soils ◽  
Genus Level ◽  
Permafrost Soils

ABSTRACTSoil fungi play a major role in terrestrial ecosystem functioning through interactions with soil structure, plants, micro- and mesofauna, and nutrient cycling through predation, pathogenesis, mutualistic, and saprotrophic roles. The diversity of soil fungi was assessed by sequencing their 28S rRNA gene in Alaskan permafrost and Oklahoma tallgrass prairie soils at experimental sites where the effect of climate warming is under investigation. A total of 226,695 reads were classified into 1,063 genera, covering 62% of the reference data set. Using the Bayesian Classifier offered by the Ribosomal Database Project (RDP) with 50% bootstrapping classification confidence, approximately 70% of sequences were returned as “unclassified” at the genus level, although the majority (∼65%) were classified at the class level, which provided insight into these lesser-known fungal lineages. Those unclassified at the genus level were subjected to BLAST analysis against the ARB-SILVA database, where ∼50% most closely matched nonfungal taxa. Compared to the more abundant sequences, a higher proportion of rare operational taxonomic units (OTU) were successfully classified to genera at 50% bootstrap confidence, indicating that the fungal rare biosphere in these sites is not composed of sequencing artifacts. There was no significant effect after 1 year of warming on the fungal community structure at both sites, except perhaps for a few minor members, but there was a significant effect of sample depth in the permafrost soils. Despite overall significant community structure differences driven by variations in OTU dominance, the prairie and permafrost soils shared 90% and 63% of all fungal sequences, respectively, indicating a fungal “seed bank” common between both sites.

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