Microbial Communities
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2022 ◽  
Vol 171 ◽  
pp. 104334
Liangliang Liu ◽  
Yuanyuan Yan ◽  
Ahmad Ali ◽  
Jun Zhao ◽  
Zucong Cai ◽  

PalZ ◽  
2021 ◽  
Pablo Suarez-Gonzalez ◽  
Joachim Reitner

AbstractOoids (subspherical particles with a laminated cortex growing around a nucleus) are ubiquitous in the geological record since the Archean and have been widely studied for more than two centuries. However, various questions about them remain open, particularly about the role of microbial communities and organic matter in their formation and development. Although ooids typically occur rolling around in agitated waters, here, we describe for the first time aragonite ooids forming statically within microbial mats from hypersaline ponds of Kiritimati (Kiribati, central Pacific). Subspherical particles had been previously observed in these mats and classified as spherulites, but these particles grow around autochthonous micritic nuclei, and many of them have laminated cortices, with alternating radial fibrous laminae and micritic laminae. Thus, they are compatible with the definition of the term ‘ooid’ and are in fact very similar to many modern and fossil examples. Kiritimati ooids are more abundant and developed in some ponds and in some particular layers of the microbial mats, which leads to the discussion and interpretation of their formation processes as product of mat evolution, through a combination of organic and environmental factors. Radial fibrous laminae are formed during periods of increased supersaturation, either by metabolic or environmental processes. Micritic laminae are formed in closer association with the mat exopolymer (EPS) matrix, probably during periods of lower supersaturation and/or stronger EPS degradation. Therefore, this study represents a step forward in the understanding of ooid development as influenced by microbial communities, providing a useful analogue for explaining similar fossil ooids.

Shi‐qi An ◽  
Robert Hull ◽  
Aline Metris ◽  
Paul Barrett ◽  
Jeremy Webb ◽  

2021 ◽  
Vol 40 ◽  
Tracy A. Romano ◽  
Laura A. Thompson ◽  
Maureen V. Driscoll ◽  
Ebru Unal ◽  
Allison D. Tuttle ◽  

Aquaria that care for and maintain belugas (Delphinapterus leucas) under professional care have the opportunity to contribute to the conservation of wild belugas through research, expertise in animal care and husbandry, and engaging and educating the public about threats to the species’ health and population sustainability. In an aquarium setting, belugas can be studied under controlled conditions, with known variables that are often difficult to discern when studying wild belugas. Information on nutrition, health status and environmental parameters can be easily obtained in a controlled setting. Biological samples are collected from professionally trained whales that voluntarily participate in informative experimental paradigms. Research studies in aquaria seek to contribute to the recovery and management of endangered beluga populations, such as those in Cook Inlet. Mystic Aquarium’s efforts are presented as a case study. Key research priorities address action items in the Cook Inlet Beluga Recovery Plan and include: (1) understanding the beluga immune system, microbial communities, pathogens and disease; (2) development of non-invasive methods for assessing reproductive status, body condition and health in wild whales; (3) investigation of diving physiology and the impact of altered dive patterns on health; (4) understanding reproduction, a key to recovery and sustainability of wild populations; (5) development and testing of new technologies for tracking and monitoring whales and habitat use; and (6) understanding how noise affects beluga hearing, behaviour and physiology. Expertise in animal handling, behaviour and nutrition contribute to rescue, rehabilitation and capture release efforts. Moreover, ‘students’ of all ages have the opportunity to be engaged, educated and contribute to beluga conservation.

Jesus Carrera ◽  
Maarten W. Saaltink ◽  
Joaquim Soler-Sagarra ◽  
Jingjing Wang ◽  
Cristina Valhondo

Reactive transport (RT) couples bio-geo-chemical reactions and transport. RT is important to understand numerous scientific questions and solve some engineering problems. RT is highly multidisciplinary, which hinders the development of a body of knowledge shared by RT modelers and developers. The goal of this paper is to review the basic conceptual issues shared by all RT problems, so as to facilitate advance along the current frontier: biochemical reactions. To this end, we review the basic equations to point that chemical systems are controlled by the set of equilibrium reactions, which are easy to model, but whose rate is controlled by mixing. Since mixing is not properly represented by the standard advection-dispersion equation (ADE), we conclude that this equation is poor for RT. This leads us to review alternative transport formulations, and the methods to solve RT problems using both the ADE and alternative equations. Since equilibrium is easy, difficulties arise for kinetic reactions, which is especially true for biochemistry, where numerous frontiers are open (how to represent microbial communities, impact of genomics, effect of biofilms on flow and transport, etc.). We conclude with the basic 10 issues that we consider fundamental for any conceptually sound RT effort.

2021 ◽  
Karley Campbell ◽  
Ilkka Matero ◽  
Christopher Bellas ◽  
Thomas Turpin-Jelfs ◽  
Philipp Anhaus ◽  

AbstractSea ice continues to decline across many regions of the Arctic, with remaining ice becoming increasingly younger and more dynamic. These changes alter the habitats of microbial life that live within the sea ice, which support healthy functioning of the marine ecosystem and provision of resources for human-consumption, in addition to influencing biogeochemical cycles (e.g. air–sea CO2 exchange). With the susceptibility of sea ice ecosystems to climate change, there is a pressing need to fill knowledge gaps surrounding sea ice habitats and their microbial communities. Of fundamental importance to this goal is the development of new methodologies that permit effective study of them. Based on outcomes from the DiatomARCTIC project, this paper integrates existing knowledge with case studies to provide insight on how to best document sea ice microbial communities, which contributes to the sustainable use and protection of Arctic marine and coastal ecosystems in a time of environmental change.

2021 ◽  
Michelle M McKnight ◽  
Josh D Neufeld

Nitrification by aquarium biofilters transforms toxic ammonia waste (NH3/NH4+) to less toxic nitrate (NO3-) via nitrite (NO2-). Ammonia oxidation is mediated by ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and the recently discovered complete ammonia oxidizing (comammox) Nitrospira. Prior to the discovery of comammox Nitrospira, previous research revealed that AOA dominate among ammonia oxidizers in freshwater biofilters. Here, we characterized the composition of aquarium filter microbial communities and quantified the abundance of all three known groups of ammonia oxidizers. Aquarium biofilter and water samples were collected from representative freshwater and saltwater systems in Southwestern Ontario, Canada. Using extracted DNA, we performed 16S rRNA gene sequencing and quantitative PCR (qPCR) to assess community composition and quantify the abundance of amoA genes, respectively. Our results show that aquarium biofilter microbial communities were consistently represented by putative heterotrophs of the Proteobacteria and Bacteroides phyla, with distinct profiles associated with fresh versus saltwater biofilters. Among nitrifiers, comammox Nitrospira amoA genes were detected in all 38 freshwater aquarium biofilter samples and were the most abundant ammonia oxidizer in 30 of these samples, with the remaining biofilters dominated by AOA, based on amoA gene abundances. In saltwater biofilters, AOA or AOB were differentially abundant, with no comammox Nitrospira detected. These results demonstrate that comammox Nitrospira play an important role in biofilter nitrification that has been previously overlooked and such microcosms are useful for exploring the ecology of nitrification for future research.

Sakcham Bairoliya ◽  
Jonas Koh Zhi Xiang ◽  
Bin Cao

Environmental DNA, i.e., DNA directly extracted from environmental samples, has been applied to understand microbial communities in the environments and to monitor contemporary biodiversity in the conservation context. Environmental DNA often contains both intracellular DNA (iDNA) and extracellular DNA (eDNA). eDNA can persist in the environment and complicate environmental DNA sequencing-based analyses of microbial communities and biodiversity. Although several studies acknowledged the impact of eDNA on DNA-based profiling of environmental communities, eDNA is still being neglected or ignored in most studies dealing with environmental samples. In this article, we summarize key findings on eDNA in environmental samples and discuss the methods used to extract and quantify eDNA as well as the importance of eDNA on the interpretation of experimental results. We then suggest several factors to consider when designing experiments and analyzing data to negate or determine the contribution of eDNA to environmental DNA-based community analyses. This field of research will be driven forward by: (i) carefully designing environmental DNA extraction pipelines by taking into consideration technical details in methods for eDNA extraction/removal and membrane-based filtration and concentration; (ii) quantifying eDNA in extracted environmental DNA using multiple methods including qPCR and fluorescent DNA binding dyes; (iii) carefully interpretating effect of eDNA on DNA-based community analyses at different taxonomic levels; and (iv) when possible, removing eDNA from environmental samples for DNA-based community analyses.

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