Riparian floodplains are important regions for biogeochemical cycling, including nitrogen. Here, we present MAGs from nitrifying microorganisms, including ammonia-oxidising archaea (AOA) and comammox bacteria from Slate River (SR) floodplain sediments (Crested Butte, CO, US). Additionally, we explore MAGs from potential nitrite-oxidising bacteria (NOB) from the Nitrospirales. AOA diversity in SR is lower than observed in other western US floodplain sediments and Nitrosotalea-like lineages such as the genus TA-20 are the dominant AOA. No ammonia-oxidising bacteria (AOB) MAGs were recovered. Microorganisms from the Palsa-1315 genus (clade B comammox) are the most abundant ammonia-oxidizers in SR floodplain sediments. Established NOB are conspicuously absent; however, we recovered MAGs from uncultured lineages of the NS-4 family (Nitrospirales) and Nitrospiraceae that we propose as putative NOB. Nitrite oxidation may be carried out by organisms sister to established Nitrospira NOB lineages based on the genomic content of uncultured Nitrospirales clades. Nitrifier MAGs recovered from SR floodplain sediments harbour genes for using alternative sources of ammonia, such as urea, cyanate, biuret, triuret and nitriles. The SR floodplain therefore appears to be a low ammonia flux environment that selects for oligotrophic nitrifiers.
Various morphotypes of large filamentous bacteria were isolated through micromanipulation from sulphidic sediment mats in the Bay of Concepción, central Chile. This study employed DNA amplification, whole-genome sequencing and bioinformatics analyses to unveil the taxonomic and genomic features of previously unidentified bacteria. The results revealed several novel genera, families and species, including three specimens belonging to Beggiatoales (Beggiatoaceae family), five to Desulfobacterales (Desulfobacteraceae family), two to the Chloroflexi phylum and one to the phylum Firmicutes. Metabolically, Beggiatoaceae bacteria exhibit a flexible and versatile genomic repertoire, enabling them to adapt to variable conditions at the sediment–water interface. All the bacteria demonstrated a mixotrophic mode, gaining energy from both inorganic and organic carbon sources. Except for the Firmicutes bacterium, all others displayed the ability to grow chemolithoautotrophically using H2 and CO2. Remarkably, the reverse tricarboxylic acid (rTCA) and Calvin–Benson–Bassham (CBB) pathways coexisted in one Beggiatoaceae bacterium. Additionally, various defence systems, such as CRISPR-Cas, along with evidence of viral interactions, have been identified. These defence mechanisms suggest that large filamentous bacteria inhabiting sulphidic sediments frequently encounter bacteriophages. Thus, robust defence mechanisms coupled with multicellularity may determine the survival or death of these large bacteria.
In denitrifying bacteria, nitric oxide (NO) is an electron acceptor and a free intermediate produced during anaerobic respiration. NO is also a signal for transcriptional regulation of the genes encoding nitrite (Nir), nitric oxide (Nor) and nitrous oxide reductases (N2OR). We hypothesise that the timing and strength of the NO signal necessary for full nir expression are key factors in the bet-hedging strategy of Paracoccus denitrificans, and that systems scavenging NO under hypoxia reduce the probability of nir induction. We show that the flavohemoglobin Hmp scavenges NO in aerobic cultures and that hmp is regulated by an NsrR-type repressor. Using a strain with an mCherry-nirS fusion, we found a clear, negative effect of Hmp on initial nir expression. Deletion of norCB eliminated bet-hedging, but the elevated NO levels in co-cultures with the wild type did not abolish bet-hedging in the wild type cells. Our results demonstrate clear roles for Hmp and Nor in regulating the expression of nirS through NO scavenging, while suggesting that the trigger for nir induction is not NO itself, but rather an intracellularly generated derivative. Our findings have important implications for understanding the regulatory network controlling the transition to anaerobic respiration.
Pelagic particle-associated bacterioplankton play crucial roles in marine ecosystems, influencing biogeochemical cycling and ecosystem functioning. However, their diversity, composition, and dynamics remain poorly understood, particularly in unique environments such as the Red Sea. In this study, we employed eDNA metabarcoding to comprehensively characterise bacterioplankton communities associated with pelagic particles in a three-dimensional assessment spanning depths from the surface to a depth of 2300 m along the full length of the eastern Red Sea within the exclusive economic zone of the Kingdom of Saudi Arabia. Our results reveal a diverse assemblage of taxa, with Pseudomonadota, Cyanobacteriota, and Planctomycetota being the dominant phyla. We identified pronounced spatial variability in community composition among five major Red Sea geographical regions, with a third of all amplicon sequence variants being unique to the Southern Red Sea in contrast to a relatively homogenous distribution along the water column depth gradient. Our findings contribute to a deeper understanding of microbial ecology in the Red Sea and provide valuable insights into the factors governing pelagic particle-associated bacterioplankton communities in this basin.
Bacteriophages (phages) are viruses that infect and lyse bacteria and have the potential for controlling bacterial diseases. Isolation of phages targeting the cherry pathogen Pseudomonas syringae pv. syringae (Pss) led to five distinct phage genotypes. Building on previous in vitro coevolution experiments, the coevolution of the five phages (individually and as a cocktail) with Pss on cherry leaves was conducted in glasshouse and field experiments. Phages effectively reduced Pss numbers on detached leaves, with no evidence of phage resistance emerging in the bacterial population. Field application of phages in a cherry orchard in Southeast England evaluated phage survival, viability and impact on bacterial populations and the microbial community. The bacterial population and phages persisted in the leaf and shoot environment as long as the bacterial host was present. In contrast to in vitro studies, the plant environment constrained the emergence of phage resistant Pss populations. Application of phage cocktail in the orchard did not affect the cherry leaf microbiome. These observations provide essential knowledge for using phage treatments to control bacterial diseases while minimising the impact on the plant microbiome, highlighting phages' potential to safely control bacterial diseases in trees.
Climate change has exposed desert ecosystems to frequent extreme disturbances, including wet-dry cycles and freeze–thaw events, which accelerate desertification on a global scale. The limited nutrient availability characteristic of these ecosystems may constrain microbial survival and growth, making them more vulnerable to environmental perturbations and stressors. However, how nutrient availability modulates the stability of soil ecological communities and functions in desert ecosystems remains poorly understood. In this study, we examined how nutrient addition, applied either before or after disturbances, affects the resistance of bacterial communities and multifunctionality to drought and freeze events in desert ecosystems. Our findings revealed that freeze–thaw events, rather than drought, significantly reduced bacterial diversity, with all disturbances altering the community structure. Pre-disturbance nutrient addition notably improved the resistance of soil bacterial diversity and community composition to disturbances, which played a critical role in maintaining multifunctionality in desert ecosystems. This enhanced bacterial resistance was strongly associated with increased bacterial network complexity and the enrichment of disturbance-tolerant taxa. Our results highlight the pivotal role of nutrient availability in stabilising soil bacterial communities and multifunctionality under extreme climatic conditions in desert ecosystems. These findings offer valuable insights and practical strategies for the ecological protection and management of desertification.
Oil reservoirs are important hydrocarbon-rich environments, where the addition of hydrocarbons to fumarate mediated by fumarate-adding enzymes (FAE) is one of the dominant mechanisms for anaerobic degradation of hydrocarbons. However, the currently available information about FaeA, the catalytic subunit of FAE, in in situ petroleum reservoirs is limited. Here, we investigated the diversity of FaeA and FaeA-harbouring microbes in oil reservoirs and compared them with marine sediments. We obtained 67 FaeA clusters and 46 FaeA-harbouring MAGs from oil reservoirs. Most FaeA sequences and all FaeA-containing microbes were endemic and unique. In oil reservoirs, FaeA sequences were affiliated with Archaeoglobus and 13 bacterial phyla. Fermentative metabolism was a common lifestyle amongst these organisms. Genomes assigned to Desulfobacterota, Caldatribacteriota and Firmicutes_B were the most diverse and prevalent, while Desulfobacterota and Chloroflexota were dominant in marine. Microbial community diversity at the phylum level was strongly related to FaeA in oil reservoirs but not in marine. This suggested that the ability of anaerobic hydrocarbon biodegradation may shape community structure in oil reservoirs. Together, this study provided systematic and comprehensive information regarding the high diversity of FaeA and FaeA-containing anaerobic hydrocarbon degraders in oil reservoirs and underlined the difference between hydrocarbon-rich environments of oil reservoirs and marine.
Warming seawater temperatures and low dissolved inorganic nitrogen (DIN) levels are environmental stressors that affect the health and abundance of marine macroalgae and their microbiomes. Nereocystis luetkeana, a canopy-forming species of brown algae that forms critical habitat along the Pacific coast, has declined in regions impacted by these synergistic stressors. Little is known about how these environmental factors affect the microbiome of N. luetkeana, which could affect nutrient availability, vitamin production, and stress response for the host. We experimentally tested the interactive effects of three seawater temperatures (13°C, 16°C, 21°C) crossed with abundant and replete DIN levels on the diversity and composition of blade-associated microbiomes from two spatially separated kelp host populations. We hypothesised that kelp microbiomes exposed to high temperatures and low DIN would experience the lowest diversity. Contrary to our hypothesis, the highest temperature treatment resulted in the largest increase in microbial diversity, and microbiomes in all temperature treatments experienced a decrease in previously dominant taxa. Temperature had a larger effect than DIN on the kelp microbiome in all cases. The disruption to the kelp microbiome across all temperatures, especially at the highest temperature, suggests that the effects of warming on N. luetkeana extend to the microbiome.
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