Syntrophic consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) consume large amounts of methane and serve as the foundational microorganisms in marine methane ...seeps. Despite their importance in the carbon cycle, research on the physiology of ANME-SRB consortia has been hampered by the slow growth and complex physicochemical environment the consortia inhabit. Here, we report successful sediment-free enrichment of ANME-SRB consortia from deep-sea methane seep sediments in the Santa Monica Basin, California. Anoxic Percoll density gradients and size-selective filtration were used to separate ANME-SRB consortia from sediment particles and single cells to accelerate the cultivation process. Over a 3-year period, a subset of the sediment-associated ANME and SRB lineages, predominantly comprised of ANME-2a/2b ("
Methanocomedenaceae") and their syntrophic bacterial partners, SEEP-SRB1/2, adapted and grew under defined laboratory conditions. Metagenome-assembled genomes from several enrichments revealed that ANME-2a, SEEP-SRB1, and
in different enrichments from the same inoculum represented distinct species, whereas other coenriched microorganisms were closely related at the species level. This suggests that ANME, SRB, and
are more genetically diverse than other members in methane seeps. Flow cytometry sorting and sequencing of cell aggregates revealed that
,
, and SEEP-SRB1 were overrepresented in multiple ANME-2a cell aggregates relative to the bulk metagenomes, suggesting they were physically associated and possibly interacting. Overall, this study represents a successful case of selective cultivation of anaerobic slow-growing microorganisms from sediments based on their physical characteristics, introducing new opportunities for detailed genomic, physiological, biochemical, and ecological analyses.
Biological anaerobic oxidation of methane (AOM) coupled with sulfate reduction represents a large methane sink in global ocean sediments. Methane consumption is carried out by syntrophic archaeal-bacterial consortia and fuels a unique ecosystem, yet the interactions in these slow-growing syntrophic consortia and with other associated community members remain poorly understood. The significance of this study is the establishment of sediment-free enrichment cultures of anaerobic methanotrophic archaea and sulfate-reducing bacteria performing AOM with sulfate using selective cultivation approaches based on size, density, and metabolism. By reconstructing microbial genomes and analyzing community composition of the enrichment cultures and cell aggregates, we shed light on the diversity of microorganisms physically associated with AOM consortia beyond the core syntrophic partners. These enrichment cultures offer simplified model systems to extend our understanding of the diversity of microbial interactions within marine methane seeps.
Surveillance for control of antimicrobial resistance Tacconelli, Evelina; Sifakis, Frangiscos; Harbarth, Stephan ...
The Lancet infectious diseases,
March 2018, 2018-03-00, 20180301, 2018-03, Letnik:
18, Številka:
3
Journal Article
Recenzirano
Odprti dostop
Antimicrobial resistance poses a growing threat to public health and the provision of health care. Its surveillance should provide up-to-date and relevant information to monitor the appropriateness ...of therapy guidelines, antibiotic formulary, antibiotic stewardship programmes, public health interventions, infection control policies, and antimicrobial development. In Europe, although the European Antimicrobial Resistance Surveillance Network provides annual reports on monitored resistant bacteria, national surveillance efforts are still fragmented and heterogeneous, and have substantial structural problems and issues with laboratory data. Most incidence and prevalence data cannot be linked with relevant epidemiological, clinical, or outcome data. Genetic typing, to establish whether trends of antimicrobial resistance are caused by spread of resistant strains or by transfer of resistance determinants among different strains and species, is not routinely done. Furthermore, laboratory-based surveillance using only clinical samples is not likely to be useful as an early warning system for emerging pathogens and resistance mechanisms. Insufficient coordination of surveillance systems of human antimicrobial resistance with animal surveillance systems is even more concerning. Because results from food surveillance are considered commercially sensitive, they are rarely released publicly by regulators. Inaccurate or incomplete surveillance data delay a translational approach to the threat of antimicrobial resistance and inhibit the identification of relevant target microorganisms and populations for research and the revitalisation of dormant drug-discovery programmes. High-quality, comprehensive, and real-time surveillance data are essential to reduce the burden of antimicrobial resistance. Improvement of national antimicrobial resistance surveillance systems and better alignment between human and veterinary surveillance systems in Europe must become a scientific and political priority, coordinated with international stakeholders within a global approach to reduce the burden of antimicrobial resistance.
Microbial consortia are a promising alternative to monocultures of genetically modified microorganisms for complex biotransformations. We developed a versatile consortium-based strategy for the ...direct conversion of lignocellulose to short-chain fatty acids, which included the funneling of the lignocellulosic carbohydrates to lactate as a central intermediate in engineered food chains. A spatial niche enabled in situ cellulolytic enzyme production by an aerobic fungus next to facultative anaerobic lactic acid bacteria and the product-forming anaerobes.
,
, or
were integrated into the lactate platform to produce 196 kilograms of butyric acid per metric ton of beechwood. The lactate platform demonstrates the benefits of mixed cultures, such as their modularity and their ability to convert complex substrates into valuable biochemicals.
Multicellular organisms, including plants, are colonized by microorganisms, some of which are beneficial to growth and health. The assembly rules for establishing plant microbiota are not well ...understood, and neither is the extent to which their members interact. We conducted drop-out and late introduction experiments by inoculating Arabidopsis thaliana with synthetic communities from a resource of 62 native bacterial strains to test how arrival order shapes community structure. As a read-out we tracked the relative abundance of all strains in the phyllosphere of individual plants. Our results showed that community assembly is historically contingent and subject to priority effects. Missing strains could, to various degrees, invade an already established microbiota, which was itself resistant and remained largely unaffected by latecomers. Additionally, our results indicate that individual strains of Proteobacteria (Sphingomonas, Rhizobium) and Actinobacteria (Microbacterium, Rhodococcus) have the greatest potential to affect community structure as keystone species.
Aims
Cropland agroforestry systems are land-use systems with numerous environmental advantages over monoculture croplands including promotion of soil life. This study aimed to investigate ...tree-species and tree-distance effects on soil biota in a temperate agroforestry system.
Methods
Our study was conducted at a paired alley-cropping and monoculture cropland system. The tree rows of the agroforestry system comprised of blocks of poplar Fritzi Pauley, poplar Max 1 or black locust. Within the agroforestry system, soil microbial and earthworm communities were collected along transects spanning from the center of the tree rows into the crop rows. Archaea, bacteria, and fungi were quantified using real-time PCR. The community composition of fungi and earthworms was deciphered using amplicon sequencing and morphological identification, respectively.
Results
Tree rows promoted the abundance of bacteria and earthworms, which we attribute mainly to tree litter input and the absence of tillage. Fungal community composition was altered by the tree rows, resulting in an increased proportion of ectomycorrhizal fungi in the tree-row associated mycobiome. The proportion of
Blumeria graminis,
the causal agent of powdery mildew, increased with increasing distance from the trees. We suggest that enhanced microbial antagonism, increased earthworm densities and/or altered microclimate contributed to the suppression of
B. graminis
in vicinity of the trees. Tree-species effect had a minor influence on the abundance and composition of soil communities at our study site.
Conclusions
In comparison to monoculture cropland, agroforestry benefits the abundance, diversity, and function of soil biota and may enhance soil suppressiveness.
Trophic interactions are crucial for carbon cycling in food webs. Traditionally, eukaryotic micropredators are considered the major micropredators of bacteria in soils, although bacteria like ...myxobacteria and Bdellovibrio are also known bacterivores. Until recently, it was impossible to assess the abundance of prokaryotes and eukaryotes in soil food webs simultaneously. Using metatranscriptomic three-domain community profiling we identified pro- and eukaryotic micropredators in 11 European mineral and organic soils from different climes. Myxobacteria comprised 1.5-9.7% of all obtained SSU rRNA transcripts and more than 60% of all identified potential bacterivores in most soils. The name-giving and well-characterized predatory bacteria affiliated with the Myxococcaceae were barely present, while Haliangiaceae and Polyangiaceae dominated. In predation assays, representatives of the latter showed prey spectra as broad as the Myxococcaceae. 18S rRNA transcripts from eukaryotic micropredators, like amoeba and nematodes, were generally less abundant than myxobacterial 16S rRNA transcripts, especially in mineral soils. Although SSU rRNA does not directly reflect organismic abundance, our findings indicate that myxobacteria could be keystone taxa in the soil microbial food web, with potential impact on prokaryotic community composition. Further, they suggest an overlooked, yet ecologically relevant food web module, independent of eukaryotic micropredators and subject to separate environmental and evolutionary pressures.
In the environment, nutrients are rarely available in a constant supply. Therefore, microorganisms require strategies to compete for limiting nutrients. In freshwater systems, ammonia-oxidizing ...archaea (AOA) and ammonia-oxidizing bacteria (AOB) compete with heterotrophic bacteria, photosynthetic microorganisms, and each other for ammonium, which AOA and AOB utilize as their sole source of energy and nitrogen. We investigated the competition between highly enriched cultures of AOA (AOA-AC1) and AOB (AOB-G5-7) for ammonium. Based on the
gene, the newly enriched archaeal ammonia oxidizer in AOA-AC1 was closely related to
spp., and the bacterial ammonia oxidizer in AOB-G5-7,
sp. strain Is79, belonged to the Nitrosomonas oligotropha group (
cluster 6a). Growth experiments in batch cultures showed that AOB-G5-7 had higher growth rates than AOA-AC1 at higher ammonium concentrations. During chemostat competition experiments under ammonium-limiting conditions, AOA-AC1 dominated the cultures, while AOB-G5-7 decreased in abundance. In batch cultures, the outcome of the competition between AOA and AOB was determined by the initial ammonium concentrations. AOA-AC1 was the dominant ammonia oxidizer at an initial ammonium concentration of 50 μM, and AOB-G5-7 was dominant at 500 μM. These findings indicate that during direct competition, AOA-AC1 was able to use ammonium that was unavailable to AOB-G5-7, while AOB-G5-7 dominated at higher ammonium concentrations. The results are in strong accordance with environmental survey data suggesting that AOA are mainly responsible for ammonia oxidation under more oligotrophic conditions, whereas AOB dominate under eutrophic conditions.
Nitrification is an important process in the global nitrogen cycle. The first step, ammonia oxidation to nitrite, can be carried out by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). In many natural environments, these ammonia oxidizers coexist. Therefore, it is important to understand the population dynamics in response to increasing ammonium concentrations. Here, we study the competition between AOA and AOB enriched from freshwater systems. The results demonstrate that AOA are more abundant in systems with low ammonium availabilities and that AOB are more abundant when the ammonium availability increases. These results will help to predict potential shifts in the community composition of ammonia oxidizers in the environment due to changes in ammonium availability.
Mixed cultures salt acclimated showed high efficiency in heterotrophic nitrification/aerobic denitrification process in hypersaline conditions. They were able to remove 80% of ammonium in ...Heterotrophic Nitrification Medium (HNM) with 12 and 14% of salt. Above these salinity, the process still had 40% ammonium removal up to 20% of salt. Chromatography analysis validated the occurrence of the heterotrophic nitrification/aerobic denitrification process in all studied salinities (6%–20% of NaCl). However, with increasing salinity, the N2 production was smaller and took longer than the unsalted control. Microbial diversity analysis of mixed cultures showed that different groups of nitrifying microorganisms were involved in ammonium removal, including heterotrophic nitrifying/aerobic denitrifying genera such as Pseudomonas, Paracoccus, Bacillus, Halomonas, Acinetobacter and Klebsiella. In addition, this analysis also revealed that the acclimation process allowed the adaptation of the microorganisms to high saline conditions and ammonium removal up to 20% of salt. This work showed that heterotrophic nitrification/aerobic denitrification process could occur in high salinity after microbiota acclimation step, and these mixed acclimated cultures have a potential for application in hypersaline effluent treatment.
•All mixed cultures performed heterotrophic nitrification-aerobic denitrification.•Mixed cultures removed 100% of ammonium with 6 and 8% of NaCl.•Mixed cultures removed 80% of ammonium with 12 and 14% of NaCl.•Acclimation process was effective to ammonium removal in high salinity.•High potential application of mixed cultures for saline wastewater treatment.
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