Chytrid fungi shape bacterial communities on model particulate organic matter

Microbial colonization and degradation of particulate organic matter (POM) are important processes that influence the structure and function of aquatic ecosystems. Although POM is readily used by aquatic fungi and bacteria, there is a limited understanding of POM-associated interactions between these taxa, particularly for early-diverging fungal lineages. Using a model ecological system with the chitin-degrading freshwater chytrid fungus Rhizoclosmatium globosum and chitin microbeads, we assessed the impacts of chytrid fungi on POM-associated bacteria. We show that the presence of chytrids on POM alters concomitant bacterial community diversity and structure, including differing responses between chytrid life stages. We propose that chytrids can act as ecosystem facilitators through saprotrophic feeding by producing ‘public goods’ from POM degradation that modify bacterial POM communities. This study suggests that chytrid fungi have complex ecological roles in aquatic POM degradation not previously considered, including the regulation of bacterial colonization, community succession and subsequent biogeochemical potential.

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Resource diversity structures aquatic bacterial communities

10.1101/387803 ◽

2018 ◽

Cited By ~ 1

Author(s):

Mario E. Muscarella ◽

Claudia M. Boot ◽

Corey D. Broeckling ◽

Jay T. Lennon

Keyword(s):

Organic Matter ◽

Bacterial Communities ◽

Alpha Diversity ◽

Structure And Function ◽

Community Diversity ◽

Resource Heterogeneity ◽

Resource Concentration ◽

And Function ◽

Resource Diversity ◽

The Relationship

ABSTRACTMicrobial diversity is strongly affected by the bottom-up effects of resource availability. However, because resource pools often exist as heterogeneous mixtures of distinct molecules, resource heterogeneity may also affect community diversity. To test this hypothesis, we surveyed bacterial communities in lakes that varied in resource concentration. In addition, we characterized resource heterogeneity in these lakes using an ecosystem metabolomics approach. Overall, resource concentration and resource heterogeneity affected bacterial resource-diversity relationships. We found strong relationships between bacterial alpha-diversity (richness and evenness) and resource concentration and richness, but richness and evenness responded in different ways. Likewise, we found associations between the composition of the bacterial community and both resource concentration and composition, but the relationship with resource composition was stronger. Last, in the surveyed communities the presence of resource generalists may have reduced the effect of resource heterogeneity on community composition. These results have implications for understanding the interactions between bacteria and organic matter and suggest that changes in organic matter composition may alter the structure and function of bacterial communities.

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Fungi and viruses as important players in microbial mats

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa187 ◽

2020 ◽

Vol 96 (11) ◽

Author(s):

Cátia Carreira ◽

Christian Lønborg ◽

Michael Kühl ◽

Ana I Lillebø ◽

Ruth-Anne Sandaa ◽

...

Keyword(s):

Organic Matter ◽

Aquatic Ecosystems ◽

Microbial Mats ◽

Freshwater Ecosystems ◽

Food Web Structure ◽

Element Cycling ◽

Functional Roles ◽

Web Structure ◽

Experimental Approaches ◽

And Function

ABSTRACT Microbial mats are compacted, surface-associated microbial ecosystems reminiscent of the first living communities on early Earth. While often considered predominantly prokaryotic, recent findings show that both fungi and viruses are ubiquitous in microbial mats, albeit their functional roles remain unknown. Fungal research has mostly focused on terrestrial and freshwater ecosystems where fungi are known as important recyclers of organic matter, whereas viruses are exceptionally abundant and important in aquatic ecosystems. Here, viruses have shown to affect organic matter cycling and the diversity of microbial communities by facilitating horizontal gene transfer and cell lysis. We hypothesise fungi and viruses to have similar roles in microbial mats. Based on the analysis of previous research in terrestrial and aquatic ecosystems, we outline novel hypotheses proposing strong impacts of fungi and viruses on element cycling, food web structure and function in microbial mats, and outline experimental approaches for studies needed to understand these interactions.

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Selective bacterial colonization processes on polyethylene waste samples in an abandoned landfill site

Scientific Reports ◽

10.1038/s41598-019-50740-w ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 9

Author(s):

Edoardo Puglisi ◽

Francesco Romaniello ◽

Serena Galletti ◽

Enrico Boccaleri ◽

Alberto Frache ◽

...

Keyword(s):

Bacterial Communities ◽

Bacterial Colonization ◽

Chemical Properties ◽

Microbial Colonization ◽

Β Diversity ◽

Physico Chemical ◽

Plastic Type ◽

Plastic Wastes ◽

Ft Raman Spectroscopy ◽

Degradation Degree

Abstract The microbial colonization of plastic wastes has been extensively studied in marine environments, while studies on aged terrestrial wastes are scarce, and mostly limited to the isolation of plastic-degrading microorganisms. Here we have applied a multidisciplinary approach involving culturomics, next-generation sequencing analyses and fine-scale physico-chemical measurements to characterize plastic wastes retrieved in landfill abandoned for more than 35 years, and to assess the composition of bacterial communities thriving as biofilms on the films’ surfaces. All samples were characterized by different colors but were all of polyethylene; IR and DSC analyses identified different level of degradation, while FT-Raman spectroscopy and X-ray fluorescence further assessed the degradation level and the presence of pigments. Each plastic type harbored distinct bacterial communities from the others, in agreement with the differences highlighted by the physico-chemical analyses. Furthermore, the most degraded polyethylene films were found to host a bacterial community more similar to the surrounding soil as revealed by both α- and β-diversity NGS analyses. This work confirms the novel hypothesis that different polyethylene terrestrial waste samples select for different bacterial communities, and that structure of these communities can be correlated with physico-chemical properties of the plastics, including the degradation degree.

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Distribution of Archaeal and Bacterial communities in a subtropical reservoir

Acta Limnologica Brasiliensia ◽

10.1590/s2179-975x3615 ◽

2015 ◽

Vol 27 (4) ◽

pp. 411-420 ◽

Cited By ~ 1

Author(s):

Laís Américo Soares ◽

André Cordeiro Alves Dos Santos ◽

Iolanda Cristina Silveira Duarte ◽

Emiliana Manesco Romagnoli ◽

Maria do Carmo Calijuri

Keyword(s):

Organic Matter ◽

Nutrient Cycling ◽

Microbial Communities ◽

Water Column ◽

Bacterial Communities ◽

Aquatic Ecosystems ◽

Metabolic Plasticity ◽

Environmental Process ◽

Ecological Importance ◽

The Relationship

Abstract Aim: Microbial communities play a central role in environmental process such as organic matter mineralization and the nutrient cycling process in aquatic ecosystems. Despite their ecological importance, variability of the structure of archaeal and bacterial communities in freshwater remains understudied. Methods In the present study we investigated the richness and density of archaea and bacteria in the water column and sediments of the Itupararanga Reservoir. We also evaluated the relationship between the communities and the biotic and abiotic characteristics. Samples were taken at five depths in the water column next to the dam and three depths next to the reservoir entrance. Results PCR-DGGE evaluation of the archaeal and bacterial communities showed that both were present in the water column, even in oxygenated conditions. Conclusions The density of the bacteria (qPCR) was greater than that of the archaea, a result of the higher metabolic plasticity of bacteria compared with archaea.

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Interspecies bacterial competition regulates community assembly in the C. elegans intestine

The ISME Journal ◽

10.1038/s41396-021-00910-4 ◽

2021 ◽

Author(s):

Anthony Ortiz ◽

Nicole M. Vega ◽

Christoph Ratzke ◽

Jeff Gore

Keyword(s):

Community Assembly ◽

Bacterial Communities ◽

Mapk Pathway ◽

Dominant Role ◽

Bacterial Species ◽

Environmental Filtering ◽

Community Diversity ◽

Interspecies Interactions ◽

C Elegans ◽

And Function

AbstractFrom insects to mammals, a large variety of animals hold in their intestines complex bacterial communities that play an important role in health and disease. To further our understanding of how intestinal bacterial communities assemble and function, we study the C. elegans microbiota with a bottom-up approach by feeding this nematode with bacterial monocultures as well as mixtures of two to eight bacterial species. We find that bacteria colonizing well in monoculture do not always do well in co-cultures due to interspecies bacterial interactions. Moreover, as community diversity increases, the ability to colonize the worm gut in monoculture becomes less important than interspecies interactions for determining community assembly. To explore the role of host–microbe adaptation, we compare bacteria isolated from C. elegans intestines and non-native isolates, and we find that the success of colonization is determined more by a species’ taxonomy than by the isolation source. Lastly, by comparing the assembled microbiotas in two C. elegans mutants, we find that innate immunity via the p38 MAPK pathway decreases bacterial abundances yet has little influence on microbiota composition. These results highlight that bacterial interspecies interactions, more so than host–microbe adaptation or gut environmental filtering, play a dominant role in the assembly of the C. elegans microbiota.

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The neglected part of the microbiome: Prophage TJ1 regulates the bacterial community of the metaorganism Hydra

10.1101/607325 ◽

2019 ◽

Author(s):

Janina Lange ◽

Sebastian Fraune ◽

Thomas C.G. Bosch ◽

Tim Lachnit

Keyword(s):

Bacterial Community ◽

Bacterial Communities ◽

Bacterial Colonization ◽

Bacterial Community Composition ◽

Broad Host Range ◽

The Stability ◽

And Function ◽

Multicellular Organisms

AbstractMany multicellular organisms are closely associated with a specific bacterial community and therefore considered “metaorganisms”. Controlling the bacterial community composition is essential for the stability and function of metaorganisms, but the factors contributing to the maintenance of host specific bacterial colonization are poorly understood. Here we demonstrate that in Hydra the most dominant bacterial colonizer Curvibacter sp. is associated with an intact prophage which can be induced by different environmental stressors both in vitro and in vivo. Differences in the induction capacity of Curvibacter phage TJ1 in culture (in vitro) and on Hydra (in vivo) imply that the habitat of the prokaryotic host and/or bacterial frequency dependent factors influence phage inducibility. Moreover, we show that phage TJ1 features a broad host range against other bacterial colonizer and is directly capable to affect bacterial colonization on Hydra. From these results we conclude that prophages are hidden part of the microbiome interfering with bacteria-bacteria interactions and have the potential to influence the composition of host associated bacterial communities.

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Algal Exudates and Stream Organic Matter Influence the Structure and Function of Denitrifying Bacterial Communities

Microbial Ecology ◽

10.1007/s00248-012-0091-1 ◽

2012 ◽

Vol 64 (4) ◽

pp. 881-892 ◽

Cited By ~ 18

Author(s):

Kathryn N. Kalscheur ◽

Miguel Rojas ◽

Christopher G. Peterson ◽

John J. Kelly ◽

Kimberly A. Gray

Keyword(s):

Organic Matter ◽

Bacterial Communities ◽

Structure And Function ◽

And Function ◽

Algal Exudates

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High Frequency of Low-Virulent Microorganisms Detected by Sonication of Implanted Pulse Generators: So What?

Stereotactic and Functional Neurosurgery ◽

10.1159/000517472 ◽

2021 ◽

pp. 1-6

Author(s):

Philipp Spindler ◽

Katharina Faust ◽

Tobias Finger ◽

Gerd-Helge Schneider ◽

Simon Bayerl ◽

...

Keyword(s):

Bacterial Colonization ◽

Clinical Signs ◽

Microbial Colonization ◽

Associated Bacteria ◽

Pulse Generators ◽

Replacement Surgery ◽

Asymptomatic Patients ◽

Cutibacterium Acnes ◽

The Impact

Introduction: Deep brain stimulation (DBS) has become a well-established treatment modality for a variety of conditions over the last decades. Multiple surgeries are an essential part in the postoperative course of DBS patients if nonrechargeable implanted pulse generators (IPGs) are applied. So far, the rate of subclinical infections in this field is unknown. In this prospective cohort study, we used sonication to evaluate possible microbial colonization of IPGs from replacement surgery. Methods: All consecutive patients undergoing IPG replacement between May 1, 2019 and November 15, 2020 were evaluated. The removed hardware was investigated using sonication to detect biofilm-associated bacteria. Demographic and clinical data were analyzed. Results: A total of 71 patients with a mean (±SD) of 64.5 ± 15.3 years were evaluated. In 23 of these (i.e., 32.4%) patients, a positive sonication culture was found. In total, 25 microorganisms were detected. The most common isolated microorganisms were Cutibacterium acnes (formerly known as Propionibacterium acnes) (68%) and coagulase-negative Staphylococci (28%). Within the follow-up period (5.2 ± 4.3 months), none of the patients developed a clinical manifest infection. Discussions/Conclusions: Bacterial colonization of IPGs without clinical signs of infection is common but does not lead to manifest infection. Further larger studies are warranted to clarify the impact of low-virulent pathogens in clinically asymptomatic patients.

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Relating particulate organic matter-nitrogen (POM-N) and non-POM-N with pulse crop residues, residue management and cereal N uptake

Agronomie ◽

10.1051/agro:2002056 ◽

2002 ◽

Vol 22 (7-8) ◽

pp. 777-787 ◽

Cited By ~ 8

Author(s):

Graeme D. Schwenke ◽

Warwick L. Felton ◽

David F. Herridge ◽

Dil F. Khan ◽

Mark B. Peoples

Keyword(s):

Organic Matter ◽

Particulate Organic Matter ◽

Crop Residues ◽

N Uptake ◽

Residue Management ◽

Pulse Crop

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Macrophyte-derived detritus in shallow coastal waters contributes to suspended particulate organic matter and increases growth rates of Mytilus edulis

Marine Ecology Progress Series ◽

10.3354/meps13314 ◽

2020 ◽

Vol 644 ◽

pp. 91-103

Author(s):

D Bearham ◽

MA Vanderklift ◽

RA Downie ◽

DP Thomson ◽

LA Clementson

Keyword(s):

Organic Matter ◽

Mytilus Edulis ◽

Particulate Organic Matter ◽

Coastal Waters ◽

Gill Tissue ◽

Suspension Feeder ◽

Food Sources ◽

Suspension Feeders ◽

Blue Mussels ◽

Suspended Particulate

Benthic suspension feeders, such as bivalves, potentially have several different food sources, including plankton and resuspended detritus of benthic origin. We hypothesised that suspension feeders are likely to feed on detritus if it is present. This inference would be further strengthened if there was a correlation between δ13C of suspension feeder tissue and δ13C of particulate organic matter (POM). Since detritus is characterised by high particulate organic matter (POC):chl a ratios, we would also predict a positive correlation between POM δ13C and POC:chl a. We hypothesised that increasing depth and greater distance from shore would produce a greater nutritional reliance by experimentally transplanted blue mussels Mytilus edulis on plankton rather than macrophyte-derived detritus. After deployments of 3 mo duration in 2 different years at depths from 3 to 40 m, M. edulis sizes were positively correlated with POM concentrations. POC:chl a ratios and δ13C of POM and M. edulis gill tissue decreased with increasing depth (and greater distance from shore). δ13C of POM was correlated with δ13C of M. edulis. Our results suggest that detritus comprised a large proportion of POM at shallow depths (<15 m), that M. edulis ingested and assimilated carbon in proportion to its availability in POM, and that growth of M. edulis was higher where detritus was present and POM concentrations were higher.

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