Genome-centered omics insight into the competition and niche differentiation of Ca. Jettenia and Ca. Brocadia affiliated to anammox bacteria

The resistance and resilience provided by functional redundancy, a common feature of microbial communities, is not always advantageous. An example is nitrite oxidation in partial nitritation-anammox (PNA) reactors during wastewater treatment, where suppression of nitrite oxidizers like Nitrospira is sought. In these ecosystems, biofilms provide microhabitats with oxygen gradients, allowing the coexistence aerobic and anaerobic bacteria. We designed a disturbance experiment where PNA biofilms treating water from a high rate activated sludge process removing organic matter (mainstream wastewater), were constantly or intermittently exposed to the effluent of anaerobic sewage sludge digestion dewatering (sidestream wastewater), which has been proposed to inhibit nitrite oxidizers. With increasing sidestream exposure we observed decreased abundance, alpha-diversity, functional versatility, and hence functional redundancy, among Nitrospira in the PNA biofilms, while the opposite patterns were observed for anammox bacteria within Brocadia. At the same time, species turnover was observed for the aerobic ammonia-oxidizing Nitrosomonas populations. The different exposure regimens were associated with metagenomic assembled genomes of Nitrosomonas, Nitrospira, and Brocadia, encoding genes related to N-cycling, substrate usage, and osmotic stress response, possibly explaining the three different patterns by niche differentiation. These findings imply that disturbances can be used to manage the functional redundancy of biofilm microbiomes in a desirable direction, which should be considered when designing operational strategies for wastewater treatment.

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Precise occlusion and trophic niche differentiation indicate specialized feeding in Early Devonian jawed vertebrates

FACETS ◽

10.1139/facets-2016-0030 ◽

2017 ◽

Vol 2 (1) ◽

pp. 513-530

Author(s):

Stephanie A. Blais

Keyword(s):

Niche Differentiation ◽

Trophic Niche ◽

Feeding Strategies ◽

Micro Computed Tomography ◽

Early Devonian ◽

Jaw Function ◽

Phylogenetic Affinities ◽

Insight Into ◽

Paraphyletic Assemblage

Acanthodians may represent a paraphyletic assemblage of stem chondrichthyans, stem osteichthyans, stem gnathostomes, or some combination of the three. One of the difficulties in determining the phylogenetic affinities of this group of mostly small, spiny fishes is that several subgroups of acanthodians are represented by relatively little information in the fossil record. It is becoming increasingly apparent that to understand the evolution of gnathostomes, we must understand more about acanthodians. This study uses micro-computed tomography to test hypotheses about acanthodian jaw function, and in doing so provides insight into the form, function, and ecological role of ischnacanthiform acanthodian jaws and teeth from an extraordinary Early Devonian fossil locality in the Northwest Territories of Canada. The results of this study suggest that ischnacanthiform acanthodians may have coexisted by trophic niche differentiation, employing specialized feeding strategies during the Silurian and Early Devonian.

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Delayed fertilization facilitates flowering time diversity in Fagaceae

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2021.0115 ◽

2021 ◽

Vol 376 (1839) ◽

Cited By ~ 2

Author(s):

Akiko Satake ◽

Dave Kelly

Keyword(s):

Flowering Time ◽

Close Association ◽

Niche Differentiation ◽

Seed Predator ◽

Time Diversity ◽

Evolutionary Advantage ◽

Delayed Fertilization ◽

Temporal Niche Differentiation ◽

New Hypothesis ◽

Insight Into

Fagaceae includes typical masting species that exhibit highly synchronized and fluctuating acorn production. Fagaceae shows an interesting feature in that fertilization is delayed by several weeks to more than 1 year after pollination. Although delayed fertilization was recorded over a century ago, the evolutionary advantage of delayed fertilization is still poorly understood. Here, we present a new hypothesis that delayed fertilization facilitates temporal niche differentiation via non-overlapping flowering times among species. Comparing flowering and fruiting times in 228 species from five genera in Fagaceae, we first show that there is a close association between a wider spread of flowering times and the likelihood of a 2-year fruiting habit in which there is a long delay from pollination to fertilization. To study the coevolution of flowering time and delayed fertilization, we developed a mathematical model that incorporates the effects of competition for pollinators, seed predator satiation and unfavourable season for reproduction on fitness. The model shows that delayed fertilization facilitates the diversification of flowering time in a population, which is advantageous for animal-pollinated trees that compete over pollinators. Our new hypothesis about the coevolution of delayed fertilization and flowering time will provide new insight into the evolution of masting. This article is part of the theme issue ‘The ecology and evolution of synchronized seed production in plants’.

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Metabolic diversity and aero-tolerance in anammox bacteria from geochemically distinct aquifers

10.1101/2021.09.16.460709 ◽

2021 ◽

Author(s):

Olivia E Mosley ◽

Emilie Gios ◽

Louise Weaver ◽

Murray Close ◽

Chris Daughney ◽

...

Keyword(s):

16S Rrna ◽

Ammonia Oxidation ◽

Niche Differentiation ◽

16S Rrna Genes ◽

Rrna Genes ◽

Anammox Bacteria ◽

Ammonium Oxidation ◽

Sandy Gravel ◽

Wide Range ◽

Terrestrial Subsurface

Background: Anaerobic ammonium oxidation (anammox) is important for converting bioavailable nitrogen into dinitrogen gas, particularly in carbon poor environments. Yet, the diversity and prevalence of anammox bacteria in the terrestrial subsurface – a typically oligotrophic environment – is little understood across different geochemical conditions. To determine the distribution and activity of anammox bacteria across a range of aquifer lithologies and physicochemistries, we analysed 16S rRNA genes, metagenomes and metatranscriptomes, and quantified hydrazine synthase genes and transcripts sampled from 59 groundwater wells distributed over 1 240 km2. Results: Data indicate that anammox-associated bacteria (class Brocadiae) and the anammox process are prevalent in aquifers (identified in aquifers with sandy-gravel, sandsilt and volcanic lithologies). While Brocadiae diversity decreased with increasing DO, Brocadiae 16S rRNA genes and hydrazine synthase genes and transcripts (hydrazine synthase, hzsB) were detected across a wide range of bulk groundwater dissolved oxygen (DO) concentrations (0 – 10 mg/L). Anammox genes and transcripts (hzsB) correlated significantly with those involved in bacterial and archaeal ammonia oxidation (ammonia monooxygenase, amoA), which could represent a major source of nitrite for anammox. Differences in anammox community composition were strongly associated with DO and bore depth (and to a lesser extent pH and phosphate), revealing niche differentiation among anammox bacteria in groundwater that was largely driven by water oxygen contents, and not ammonium/nitrite. Eight Brocadiae genomes (63-95% estimated completeness) reconstructed from a subset of groundwater sites belong to 2 uncharacterized families and 6 novel species (based on average nucleotide identity). Distinct groups of these genomes dominated the anammox-associated community at dysoxic and oxic sites, further reflecting the influence of DO on Brocadiae composition. Six of the genomes (dominating dysoxic or oxic sites) have genes characteristic of anammox (hydrazine synthase and/or dehydrogenase). These genes, in addition to aerotolerance genes, belonging to four Brocadiae genomes, were transcriptionally active, although transcript numbers clearly highest in dyoxic groundwater. Conclusions: Our findings indicate anammox bacteria contribute to loss of fixed N across diverse anoxic-to-oxic aquifer conditions, and that this is likely supported by nitrite from aerobic ammonia oxidation. Results provide an insight into the distribution and activity of anammox bacteria across distinct aquifer physicochemisties.

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Growth at Low Ammonium Concentrations and Starvation Response as Potential Factors Involved in Niche Differentiation among Ammonia-Oxidizing Bacteria

Applied and Environmental Microbiology ◽

10.1128/aem.68.10.4751-4757.2002 ◽

2002 ◽

Vol 68 (10) ◽

pp. 4751-4757 ◽

Cited By ~ 131

Author(s):

Annette Bollmann ◽

Marie-José Bär-Gilissen ◽

Hendrikus J. Laanbroek

Keyword(s):

Heterotrophic Bacteria ◽

Niche Differentiation ◽

Ammonia Oxidizer ◽

Close Relative ◽

Ammonia Oxidizing Bacteria ◽

Growth Experiment ◽

Starvation Response ◽

Regeneration Time ◽

Potential Factors ◽

Insight Into

ABSTRACT In nature, ammonia-oxidizing bacteria have to compete with heterotrophic bacteria and plants for limiting amounts of ammonium. Previous laboratory experiments conducted with Nitrosomonas europaea suggested that ammonia-oxidizing bacteria are weak competitors for ammonium. To obtain a better insight into possible methods of niche differentiation among ammonia-oxidizing bacteria, we carried out a growth experiment at low ammonium concentrations with N. europaea and the ammonia oxidizer G5-7, a close relative of Nitrosomonas oligotropha belonging to Nitrosomonas cluster 6a, enriched from a freshwater sediment. Additionally, we compared the starvation behavior of the newly enriched ammonia oxidizer G5-7 to that of N. europaea. The growth experiment at low ammonium concentrations showed that strain G5-7 was able to outcompete N. europaea at growth-limiting substrate concentrations of about 10 μM ammonium, suggesting better growth abilities of the ammonia oxidizer G5-7 at low ammonium concentrations. However, N. europaea displayed a more favorable starvation response. After 1 to 10 weeks of ammonium deprivation, N. europaea became almost immediately active after the addition of fresh ammonium and converted the added ammonium within 48 to 96 h. In contrast, the regeneration time of the ammonia oxidizer G5-7 increased with increasing starvation time. Taken together, these results provide insight into possible mechanisms of niche differentiation for the ammonia-oxidizing bacteria studied. The Nitrosomonas cluster 6a member, G5-7, is able to grow at ammonium concentrations at which the growth of N. europaea, belonging to Nitrosomonas cluster 7, has already ceased, providing an advantage in habitats with continuously low ammonium concentrations. On the other hand, the ability of N. europaea to become active again after longer periods of starvation for ammonium may allow better exploitation of irregular pulses of ammonium in the environment.

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