scholarly journals Are nitrogen and carbon cycle processes impacted by common stream antibiotics? A comparative assessment of single vs. mixture exposures

PLoS ONE ◽  
2022 ◽  
Vol 17 (1) ◽  
pp. e0261714
Author(s):  
Austin D. Gray ◽  
Emily Bernhardt
Keyword(s):  
Microbial Communities ◽  
Nitrogen Cycling ◽  
Carbon Fixation ◽  
Inorganic Nitrogen ◽  
Combined Treatment ◽  
Stream Sediments ◽  
Freshwater Ecosystems ◽  
Nitrogen Transformations ◽  
Community Resistance ◽  
Mixture Treatment

A variety of antibiotics are ubiquitous in all freshwater ecosystems that receive wastewater. A wide variety of antibiotics have been developed to kill problematic bacteria and fungi through targeted application, and their use has contributed significantly to public health and livestock management. Unfortunately, a substantial fraction of the antibiotics applied to humans, pets and livestock end up in wastewater, and ultimately many of these chemicals enter freshwater ecosystems. The effect of adding chemicals that are intentionally designed to kill microbes, on freshwater microbial communities remains poorly understood. There are reasons to be concerned, as microbes play an essential role in nutrient uptake, carbon fixation and denitrification in freshwater ecosystems. Chemicals that reduce or alter freshwater microbial communities might reduce their capacity to degrade the excess nutrients and organic matter that characterize wastewater. We performed a laboratory experiment in which we exposed microbial community from unexposed stream sediments to three commonly detected antibiotics found in urban wastewater and urban streams (sulfamethoxazole, danofloxacin, and erythromycin). We assessed how the form and concentration of inorganic nitrogen, microbial carbon, and nitrogen cycling processes changed in response to environmentally relevant doses (10 μg/L) of each of these antibiotics individually and in combination. We expected to find that all antibiotics suppressed rates of microbial mineralization and nitrogen transformations and we anticipated that this suppression of microbial activity would be greatest in the combined treatment. Contrary to our expectations we measured few significant changes in microbially mediated functions in response to our experimental antibiotic dosing. We found no difference in functional gene abundance of key nitrogen cycling genes nosZ, mcrA, nirK, and amoA genes, and we measured no treatment effects on NO3- uptake or N2O, N2, CH4, CO2 production over the course of our seven-day experiment. In the mixture treatment, we measured significant increases in NH4+ concentrations over the first 24 hours of the experiment, which were indistinguishable from controls within six hours. Our results suggest remarkable community resistance to pressure antibiotic exposure poses on naïve stream sediments.

scholarly journals Transcriptional Activities of the Microbial Consortium Living with the Marine Nitrogen-Fixing Cyanobacterium Trichodesmium Reveal Potential Roles in Community-Level Nitrogen Cycling

2017 ◽  
Vol 84 (1) ◽  
Author(s):  
Michael D. Lee ◽  
Eric A. Webb ◽  
Nathan G. Walworth ◽  
Fei-Xue Fu ◽  
Noelle A. Held ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nitrogen Fixation ◽  
Microbial Communities ◽  
Nitrogen Cycling ◽  
Carbon Fixation ◽  
Community Respiration ◽  
Ecological Niches ◽  
Nitrogen Fixing ◽  
Content Type ◽  
Globally Distributed

ABSTRACTTrichodesmiumis a globally distributed cyanobacterium whose nitrogen-fixing capability fuels primary production in warm oligotrophic oceans. Like many photoautotrophs,Trichodesmiumserves as a host to various other microorganisms, yet little is known about how this associated community modulates fluxes of environmentally relevant chemical species into and out of the supraorganismal structure. Here, we utilized metatranscriptomics to examine gene expression activities of microbial communities associated withTrichodesmium erythraeum(strain IMS101) using laboratory-maintained enrichment cultures that have previously been shown to harbor microbial communities similar to those of natural populations. In enrichments maintained under two distinct CO2concentrations for ∼8 years, the community transcriptional profiles were found to be specific to the treatment, demonstrating a restructuring of overall gene expression had occurred. Some of this restructuring involved significant increases in community respiration-related transcripts under elevated CO2, potentially facilitating the corresponding measured increases in host nitrogen fixation rates. Particularly of note, in both treatments, community transcripts involved in the reduction of nitrate, nitrite, and nitrous oxide were detected, suggesting the associated organisms may play a role in colony-level nitrogen cycling. Lastly, a taxon-specific analysis revealed distinct ecological niches of consistently cooccurring major taxa that may enable, or even encourage, the stable cohabitation of a diverse community withinTrichodesmiumconsortia.IMPORTANCETrichodesmiumis a genus of globally distributed, nitrogen-fixing marine cyanobacteria. As a source of new nitrogen in otherwise nitrogen-deficient systems, these organisms help fuel carbon fixation carried out by other more abundant photoautotrophs and thereby have significant roles in global nitrogen and carbon cycling. Members of theTrichodesmiumgenus tend to form large macroscopic colonies that appear to perpetually host an association of diverse interacting microbes distinct from the surrounding seawater, potentially making the entire assemblage a unique miniature ecosystem. Since its first successful cultivation in the early 1990s, there have been questions about the potential interdependencies betweenTrichodesmiumand its associated microbial community and whether the host's seemingly enigmatic nitrogen fixation schema somehow involved or benefited from its epibionts. Here, we revisit these old questions with new technology and investigate gene expression activities of microbial communities living in association withTrichodesmium.

LDPE microplastics affect soil microbial communities and nitrogen cycling

2021 ◽  
Vol 773 ◽  
pp. 145640
Author(s):  
Lili Rong ◽  
Longfei Zhao ◽  
Leicheng Zhao ◽  
Zhipeng Cheng ◽  
Yiming Yao ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Nitrogen Cycling ◽  
Soil Microbial Communities ◽  
Soil Microbial

scholarly journals Small freshwater ecosystems with dissimilar microbial communities exhibit similar temporal patterns

2021 ◽  
Vol 30 (9) ◽  
pp. 2162-2177
Author(s):  
Gwendoline M. David ◽  
Purificación López‐García ◽  
David Moreira ◽  
Benjamin Alric ◽  
Philippe Deschamps ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Temporal Patterns ◽  
Freshwater Ecosystems

scholarly journals Nitrification–denitrification in waste stabilisation ponds: a mechanism for permanent nitrogen removal in maturation ponds

2010 ◽  
Vol 61 (5) ◽  
pp. 1137-1146 ◽  
Author(s):  
M. A. Camargo Valero ◽  
L. F. Read ◽  
D. D. Mara ◽  
R. J. Newton ◽  
T. P. Curtis ◽  
...  
Keyword(s):  
Nitrogen Removal ◽  
Inorganic Nitrogen ◽  
Isotope Analysis ◽  
Pilot Scale ◽  
Intermediate Step ◽  
Nitrogen Transformations ◽  
Waste Stabilisation Ponds ◽  
Molecular Microbiology ◽  
Denitrification Process ◽  
Ammonia Oxidising Bacteria

A pilot-scale primary maturation pond was spiked with 15N-labelled ammonia (15NH4Cl) and 15N-labelled nitrite (Na15NO2), in order to improve current understanding of the dynamics of inorganic nitrogen transformations and removal in WSP systems. Stable isotope analysis of δ15N showed that nitrification could be considered as an intermediate step in WSP, which is masked by simultaneous denitrification, under conditions of low algal activity. Molecular microbiology analysis showed that denitrification can be considered a feasible mechanism for permanent nitrogen removal in WSP, which may be supported either by ammonia-oxidising bacteria (AOB) or by methanotrophs, in addition to nitrite-oxidising bacteria (NOB). However, the relative supremacy of the denitrification process over other nitrogen removal mechanisms (e.g., biological uptake) depends upon phytoplanktonic activity.

scholarly journals The keystone species of Precambrian deep bedrock biosphere belong to <i>Burkholderiales</i> and <i>Clostridiales</i>

2015 ◽  
Vol 12 (21) ◽  
pp. 18103-18150 ◽  
Author(s):  
L. Purkamo ◽  
M. Bomberg ◽  
R. Kietäväinen ◽  
H. Salavirta ◽  
M. Nyyssönen ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Carbon Fixation ◽  
Keystone Species ◽  
Carbon Assimilation ◽  
Sugar Metabolism ◽  
Archaeal Community ◽  
Amino Sugar ◽  
Amplicon Sequencing ◽  
Fracture Zones ◽  
Crystalline Bedrock

Abstract. The bacterial and archaeal community composition and the possible carbon assimilation processes and energy sources of microbial communities in oligotrophic, deep, crystalline bedrock fractures is yet to be resolved. In this study, intrinsic microbial communities from six fracture zones from 180–2300 m depths in Outokumpu bedrock were characterized using high-throughput amplicon sequencing and metagenomic prediction. Comamonadaceae-, Anaerobrancaceae- and Pseudomonadaceae-related OTUs form the core community in deep crystalline bedrock fractures in Outokumpu. Archaeal communities were mainly composed of Methanobacteraceae-affiliating OTUs. The predicted bacterial metagenomes showed that pathways involved in fatty acid and amino sugar metabolism were common. In addition, relative abundance of genes coding the enzymes of autotrophic carbon fixation pathways in predicted metagenomes was low. This indicates that heterotrophic carbon assimilation is more important for microbial communities of the fracture zones. Network analysis based on co-occurrence of OTUs revealed the keystone genera of the microbial communities belonging to Burkholderiales and Clostridiales. Bacterial communities in fractures resemble those found from oligotrophic, hydrogen-enriched environments. Serpentinization reactions of ophiolitic rocks in Outokumpu assemblage may provide a source of energy and organic carbon compounds for the microbial communities in the fractures. Sulfate reducers and methanogens form a minority of the total microbial communities, but OTUs forming these minor groups are similar to those found from other deep Precambrian terrestrial bedrock environments.

scholarly journals Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations

mSystems ◽  
2021 ◽  
Vol 6 (3) ◽  
Author(s):  
Sarahi L. Garcia ◽  
Maliheh Mehrshad ◽  
Moritz Buck ◽  
Jackson M. Tsuji ◽  
Josh D. Neufeld ◽  
...  
Keyword(s):  
Carbon Fixation ◽  
Carbon Sources ◽  
Natural Populations ◽  
Freshwater Ecosystems ◽  
Electron Donors ◽  
Functional Ecology ◽  
Lake Ecosystems ◽  
Tropical Regions ◽  
Metabolic Versatility ◽  
Globally Distributed

ABSTRACT Photosynthetic bacteria from the class Chlorobia (formerly phylum Chlorobi) sustain carbon fixation in anoxic water columns. They harvest light at extremely low intensities and use various inorganic electron donors to fix carbon dioxide into biomass. Until now, most information on the functional ecology and local adaptations of Chlorobia members came from isolates and merely 26 sequenced genomes that may not adequately represent natural populations. To address these limitations, we analyzed global metagenomes to profile planktonic Chlorobia cells from the oxyclines of 42 freshwater bodies, spanning subarctic to tropical regions and encompassing all four seasons. We assembled and compiled over 500 genomes, including metagenome-assembled genomes (MAGs), single-amplified genomes (SAGs), and reference genomes from cultures, clustering them into 71 metagenomic operational taxonomic units (mOTUs or “species”). Of the 71 mOTUs, 57 were classified within the genus Chlorobium, and these mOTUs represented up to ∼60% of the microbial communities in the sampled anoxic waters. Several Chlorobium-associated mOTUs were globally distributed, whereas others were endemic to individual lakes. Although most clades encoded the ability to oxidize hydrogen, many lacked genes for the oxidation of specific sulfur and iron substrates. Surprisingly, one globally distributed Scandinavian clade encoded the ability to oxidize hydrogen, sulfur, and iron, suggesting that metabolic versatility facilitated such widespread colonization. Overall, these findings provide new insight into the biogeography of the Chlorobia and the metabolic traits that facilitate niche specialization within lake ecosystems. IMPORTANCE The reconstruction of genomes from metagenomes has helped explore the ecology and evolution of environmental microbiota. We applied this approach to 274 metagenomes collected from diverse freshwater habitats that spanned oxic and anoxic zones, sampling seasons, and latitudes. We demonstrate widespread and abundant distributions of planktonic Chlorobia-associated bacteria in hypolimnetic waters of stratified freshwater ecosystems and show they vary in their capacities to use different electron donors. Having photoautotrophic potential, these Chlorobia members could serve as carbon sources that support metalimnetic and hypolimnetic food webs.

scholarly journals Microbial dark carbon fixation fueled by nitrate enrichment

2021 ◽  
Author(s):  
Joseph H. Vineis ◽  
Ashley N. Bulseco ◽  
Jennifer L. Bowen
Keyword(s):  
Microbial Communities ◽  
Marine Sediments ◽  
Salt Marshes ◽  
Carbon Fixation ◽  
Niche Partitioning ◽  
Coastal Marine Sediments ◽  
Functional Relationships ◽  
Coastal Marine ◽  
Dark Carbon Fixation ◽  
The Impact

Anthropogenic nitrate amendment to coastal marine sediments can increase rates of heterotrophic mineralization and autotrophic dark carbon fixation (DCF). DCF may be favored in sediments where organic matter is biologically unavailable, leading to a microbial community supported by chemoautotrophy. Niche partitioning among DCF communities and adaptations for nitrate metabolism in coastal marine sediments remain poorly characterized, especially within salt marshes. We used genome-resolved metagenomics, phylogenetics, and comparative genomics to characterize the potential niche space, phylogenetic relationships, and adaptations important to microbial communities within nitrate enriched sediment. We found that nitrate enrichment of sediment from discrete depths between 0-25 cm supported both heterotrophs and chemoautotrophs that use sulfur oxidizing denitrification to drive the Calvin-Benson-Bassham (CBB) or reductive TCA (rTCA) DCF pathways. Phylogenetic reconstruction indicated that the nitrate enriched community represented a small fraction of the phylogenetic diversity contained in coastal marine environmental genomes, while pangenomics revealed close evolutionary and functional relationships with DCF microbes in other oligotrophic environments. These results indicate that DCF can support coastal marine microbial communities and should be carefully considered when estimating the impact of nitrate on carbon cycling in these critical habitats.

Sign in / Sign up

Export Citation Format

Share Document