Metagenome assembled genomes (MAGs), generated from sequenced 13C‐labelled DNA from 13C‐methanol enriched soils, were binned using an ensemble approach. This method produced a significantly larger ...number of higher‐quality MAGs compared to direct binning approaches. These MAGs represent both the primary methanol utilizers and the secondary utilizers labelled via cross‐feeding and predation on the labelled methylotrophs, including numerous uncultivated taxa. Analysis of these MAGs enabled the identification of multiple metabolic pathways within these active taxa that have climatic relevance relating to nitrogen, sulfur and trace gas metabolism. This includes denitrification, dissimilatory nitrate reduction to ammonium, ammonia oxidation and metabolism of organic sulfur species. The binning of viral sequence data also yielded extensive viral MAGs, identifying active viral replication by both lytic and lysogenic phages within the methanol‐enriched soils. These MAGs represent a valuable resource for characterizing biogeochemical cycling within terrestrial environments.
Ensemble binning of environmental metagenomes significantly improves the analysis of complex datasets. A re‐analysis of metagenomes, derived from labelled DNA extracted from 13C methanol‐enriched rhizosphere soils, yielded a substantial number of metagenome‐assembled genomes. This facilitated the identification of numerous biogeochemical cycling pathways, including those relevant to climate change. The binning process further revealed metagenome‐assembled genomes (MAGs) of bacterial predators and viruses, thereby uncovering trophic interactions within the enriched soils. This dataset serves as a valuable resource for characterising biogeochemical cycling within terrestrial environments.
To assess whether life existed on Mars, it is crucial to identify geochemical biosignatures that are relevant to specific Martian environments. In this paper, thermochemical modeling was used to ...investigate fluid chemistries and secondary minerals that would have evolved biotically over geological time scales in Martian fluvio‐lacustrine and evaporitic settings, and that could be used as potential inorganic biosignatures for life detection on Mars. Modeling was performed using fluid and rock chemistries relevant to Gale crater aqueous environments. Potential inorganic biosignatures were identified investigating alteration deposits found at the surface of a simulant exposed to short‐term bio‐mediated weathering and comparing experimental and modeling results. In a fluvio‐lacustrine setting (water/rock of 2000–278), models suggest that less complex mineral assemblages form during biotic basalt dissolution and subsequent brine evaporation compared to what would happen in an abiotic system. Mainly nontronite, kaolinite, and quartz form under biotic conditions, whereas celadonite, talc, and goethite would also precipitate abiotically. Quartz, sepiolite, and gypsum would precipitate from the evaporation of fluids evolved biotically, whereas nontronite, talc, zeolite, and gypsum would form in an abiotic evaporitic environment. These results could be used to distinguish products of abiotic and biotic processes, aiding the interpretation of data from Mars exploration missions.
Abstract
Microbial ecology provides insights into the ecological and evolutionary dynamics of microbial communities underpinning every ecosystem on Earth. Microbial communities can now be ...investigated in unprecedented detail, although there is still a wealth of open questions to be tackled. Here we identify 50 research questions of fundamental importance to the science or application of microbial ecology, with the intention of summarising the field and bringing focus to new research avenues. Questions are categorised into seven themes: host–microbiome interactions; health and infectious diseases; human health and food security; microbial ecology in a changing world; environmental processes; functional diversity; and evolutionary processes. Many questions recognise that microbes provide an extraordinary array of functional diversity that can be harnessed to solve real-world problems. Our limited knowledge of spatial and temporal variation in microbial diversity and function is also reflected, as is the need to integrate micro- and macro-ecological concepts, and knowledge derived from studies with humans and other diverse organisms. Although not exhaustive, the questions presented are intended to stimulate discussion and provide focus for researchers, funders and policy makers, informing the future research agenda in microbial ecology.
We identify research questions in the field of microbial ecology, with emerging themes that recognise vast microbial functions that could benefit humanity, and the need to integrate knowledge across organisms.
Methanol is the second most abundant volatile organic compound in the atmosphere, with the majority produced as a metabolic by-product during plant growth. There is a large disparity between the ...estimated amount of methanol produced by plants and the amount which escapes to the atmosphere. This may be due to utilisation of methanol by plant-associated methanol-consuming bacteria (methylotrophs). The use of molecular probes has previously been effective in characterising the diversity of methylotrophs within the environment. Here, we developed and applied molecular probes in combination with stable isotope probing to identify the diversity, abundance and activity of methylotrophs in bulk and in plant-associated soils.
Application of probes for methanol dehydrogenase genes (mxaF, xoxF, mdh2) in bulk and plant-associated soils revealed high levels of diversity of methylotrophic bacteria within the bulk soil, including Hyphomicrobium, Methylobacterium and members of the Comamonadaceae. The community of methylotrophic bacteria captured by this sequencing approach changed following plant growth. This shift in methylotrophic diversity was corroborated by identification of the active methylotrophs present in the soils by DNA stable isotope probing using
C-labelled methanol. Sequencing of the 16S rRNA genes and construction of metagenomes from the
C-labelled DNA revealed members of the Methylophilaceae as highly abundant and active in all soils examined. There was greater diversity of active members of the Methylophilaceae and Comamonadaceae and of the genus Methylobacterium in plant-associated soils compared to the bulk soil. Incubating growing pea plants in a
CO
atmosphere revealed that several genera of methylotrophs, as well as heterotrophic genera within the Actinomycetales, assimilated plant exudates in the pea rhizosphere.
In this study, we show that plant growth has a major impact on both the diversity and the activity of methanol-utilising methylotrophs in the soil environment, and thus, the study contributes significantly to efforts to balance the terrestrial methanol and carbon cycle. Video abstract.
Nitrate-dependent Fe
2+
oxidation (NDFO) is a microbially mediated process observed in many anaerobic, low-nutrient (oligotrophic) neutral–alkaline environments on Earth, which describes oxidation of ...Fe
2+
to Fe
3+
in tandem with microbial nitrate reduction. Evidence suggests that similar environments existed on Mars during the Noachian epoch (4.1–3.7 Ga) and in periodic, localised environments more recently, indicating that NDFO metabolism could have played a role in a potential early martian biosphere. In this paper, three NDFO microorganisms,
Acidovorax
sp. strain BoFeN1,
Pseudogulbenkiania
sp. strain 2002 and
Paracoccus
sp. strain KS1, were assessed for their ability to grow oligotrophically in simulated martian brines and in a minimal medium with olivine as a solid Fe
2+
source. These simulant-derived media were developed from modelled fluids based on the geochemistry of Mars sample locations at Rocknest (contemporary Mars soil), Paso Robles (sulphur-rich soil), Haematite Slope (haematite-rich soil) and a Shergottite meteorite (common basalt). The Shergottite medium was able to support growth of all three organisms, while the contemporary Mars medium supported growth of
Acidovorax
sp. strain BoFeN1 and
Pseudogulbenkiania
sp. strain 2002; however, growth was not accompanied by significant Fe
2+
oxidation. Each of the strains was also able to grow in oligotrophic minimal media with olivine as the sole Fe
2+
source. Biomineralised cells of
Pseudogulbenkiania
sp. strain 2002 were identified on the surface of the olivine, representing a potential biosignature for NDFO microorganisms in martian samples. The results suggest that NDFO microorganisms could have thrived in early martian groundwaters under oligotrophic conditions, depending on the local lithology. This can guide missions in identifying palaeoenvironments of interest for biosignature detection. Indeed, biomineralised cells identified on the olivine surface provide a previously unexplored mechanism for the preservation of morphological biosignatures in the martian geological record.
Streptomyces
species are saprophytic soil bacteria that produce a diverse array of specialized metabolites, including half of all known antibiotics. They are also rhizobacteria and plant endophytes ...that can promote plant growth and protect against disease. Several studies have shown that streptomycetes are enriched in the rhizosphere and endosphere of the model plant
Arabidopsis thaliana
. Here, we set out to test the hypothesis that they are attracted to plant roots by root exudates, and specifically by the plant phytohormone salicylate, which they might use as a nutrient source. We confirmed a previously published report that salicylate over-producing
cpr5
plants are colonized more readily by streptomycetes but found that salicylate-deficient
sid2-2
and
pad4
plants had the same levels of root colonization by
Streptomyces
bacteria as the wild-type plants. We then tested eight genome sequenced
Streptomyces
endophyte strains
in vitro
and found that none were attracted to or could grow on salicylate as a sole carbon source. We next used
13
CO
2
DNA stable isotope probing to test whether
Streptomyces
species can feed off a wider range of plant metabolites but found that
Streptomyces
bacteria were outcompeted by faster growing proteobacteria and did not incorporate photosynthetically fixed carbon into their DNA. We conclude that, given their saprotrophic nature and under conditions of high competition, streptomycetes most likely feed on more complex organic material shed by growing plant roots. Understanding the factors that impact the competitiveness of strains in the plant root microbiome could have consequences for the effective application of biocontrol strains.
Abstract
Background
Conventional methods of agricultural pest control and crop fertilisation are unsustainable. To meet growing demand, we must find ecologically responsible means to control disease ...and promote crop yields. The root-associated microbiome can aid plants with disease suppression, abiotic stress relief, and nutrient bioavailability. The aim of the present work was to profile the community of bacteria, fungi, and archaea associated with the wheat rhizosphere and root endosphere in different conditions. We also aimed to use
13
CO
2
stable isotope probing (SIP) to identify microbes within the root compartments that were capable of utilising host-derived carbon.
Results
Metabarcoding revealed that community composition shifted significantly for bacteria, fungi, and archaea across compartments. This shift was most pronounced for bacteria and fungi, while we observed weaker selection on the ammonia oxidising archaea-dominated archaeal community. Across multiple soil types we found that soil inoculum was a significant driver of endosphere community composition, however, several bacterial families were identified as core enriched taxa in all soil conditions. The most abundant of these were
Streptomycetaceae
and
Burkholderiaceae
. Moreover, as the plants senesce, both families were reduced in abundance, indicating that input from the living plant was required to maintain their abundance in the endosphere. Stable isotope probing showed that bacterial taxa within the
Burkholderiaceae
family, among other core enriched taxa such as
Pseudomonadaceae,
were able to use root exudates, but
Streptomycetaceae
were not.
Conclusions
The consistent enrichment of
Streptomycetaceae
and
Burkholderiaceae
within the endosphere, and their reduced abundance after developmental senescence, indicated a significant role for these families within the wheat root microbiome. While
Streptomycetaceae
did not utilise root exudates in the rhizosphere, we provide evidence that
Pseudomonadaceae
and
Burkholderiaceae
family taxa are recruited to the wheat root community via root exudates. This deeper understanding crop microbiome formation will enable researchers to characterise these interactions further, and possibly contribute to ecologically responsible methods for yield improvement and biocontrol in the future.
Microorganisms inhabiting hypersaline environments have received significant attention due to their ability to thrive under poly-extreme conditions, including high salinity, elevated temperatures and ...heavy metal stress. They are believed to possess biosynthetic gene clusters (BGCs) that encode secondary metabolites as survival strategy and offer potential biotechnological applications. In this study, we mined BGCs in shotgun metagenomic sequences generated from Lake Afdera, a hypersaline lake in the Afar Depression, Ethiopia. The microbiome of Lake Afdera is predominantly bacterial, with
(18.6%) and
(11.8%) being ubiquitously detected. A total of 94 distinct BGCs were identified in the metagenomic data. These BGCs are found to encode secondary metabolites with two main categories of functions: (i) potential pharmaceutical applications (nonribosomal peptide synthase NRPs, polyketide synthase, others) and (ii) miscellaneous roles conferring adaptation to extreme environment (bacteriocins, ectoine, others). Notably, NRPs (20.6%) and bacteriocins (10.6%) were the most abundant. Furthermore, our metagenomic analysis predicted gene clusters that enable microbes to defend against a wide range of toxic metals, oxidative stress and osmotic stress. These findings suggest that Lake Afdera is a rich biological reservoir, with the predicted BGCs playing critical role in the survival and adaptation of extremophiles.
The Makgadikgadi Salt Pans are the remnants of a mega paleo-lake system in the central Kalahari, Botswana. Today, the Makgadikgadi Basin is an arid to semi-arid area receiving water of meteoric ...origin during the short, wet season. Large microbial mats, which support primary production, are formed due to desiccation during the dry season. This study aimed to characterise the microbial diversity of the microbial mats and the underlying sediment. The focus was the Ntwetwe Pan, located west of the Makgadikgadi Basin. Metagenomic analyses demonstrated that the mats consisted of a high relative abundance of Cyanobacteriota (synonym Cyanobacteria) (20.50-41.47%), Pseudomonadota (synonym Proteobacteria) (15.71 to 32.18%), and Actinomycetota (synonym Actinobacteria) (8.53-32.56%). In the underlying sediments, Pseudomonadota, Actinomycetota, and Euryarchaeota represented over 70% of the community. Localised fluctuations in water content and pH did not significantly affect the microbial diversity of the sediment or the mats.
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