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Physiological limits to life in anoxic subseafloor sediment.
Orsi, WD, Schink, B, Buckel, W, Martin, WF
FEMS microbiology reviews. 2020;(2):219-231
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Abstract
In subseafloor sediment, microbial cell densities exponentially decrease with depth into the fermentation zone. Here, we address the classical question of 'why are cells dying faster than they are growing?' from the standpoint of physiology. The stoichiometries of fermentative ATP production and consumption in the fermentation zone place bounds on the conversion of old cell biomass into new. Most fermentable organic matter in deep subseafloor sediment is amino acids from dead cells because cells are mostly protein by weight. Conversion of carbon from fermented dead cell protein into methanogen protein via hydrogenotrophic and acetoclastic methanogenesis occurs at ratios of ∼200:1 and 100:1, respectively, while fermenters can reach conversion ratios approaching 6:1. Amino acid fermentations become thermodynamically more efficient at lower substrate and product concentrations, but the conversion of carbon from dead cell protein into fermenter protein is low because of the high energetic cost of translation. Low carbon conversion factors within subseafloor anaerobic feeding chains account for exponential declines in cellular biomass in the fermentation zone of anoxic sediments. Our analysis points to the existence of a life-death transition zone in which the last biologically catalyzed life processes are replaced with purely chemical reactions no longer coupled to life.
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Organic geochemical approaches to understanding early life.
Alleon, J, Summons, RE
Free radical biology & medicine. 2019;:103-112
Abstract
Here we discuss the early geological record of preserved organic carbon and the criteria that must be applied to distinguish biological from non-biological origins. Sedimentary graphite, irrespective of its isotopic composition, does not constitute a reliable biosignature because the rocks in which it is found are generally metamorphosed to the point where convincing signs of life have been erased. Rather, multiple lines of evidence, including sedimentary textures, microfossils, large accumulations of organic matter and isotopic data for co-existing carbon, nitrogen and sulfur are required before biological origin can be convincingly demonstrated.
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Ancient plant DNA in lake sediments.
Parducci, L, Bennett, KD, Ficetola, GF, Alsos, IG, Suyama, Y, Wood, JR, Pedersen, MW
The New phytologist. 2017;(3):924-942
Abstract
Contents 924 I. 925 II. 925 III. 927 IV. 929 V. 930 VI. 930 VII. 931 VIII. 933 IX. 935 X. 936 XI. 938 938 References 938 SUMMARY Recent advances in sequencing technologies now permit the analyses of plant DNA from fossil samples (ancient plant DNA, plant aDNA), and thus enable the molecular reconstruction of palaeofloras. Hitherto, ancient frozen soils have proved excellent in preserving DNA molecules, and have thus been the most commonly used source of plant aDNA. However, DNA from soil mainly represents taxa growing a few metres from the sampling point. Lakes have larger catchment areas and recent studies have suggested that plant aDNA from lake sediments is a more powerful tool for palaeofloristic reconstruction. Furthermore, lakes can be found globally in nearly all environments, and are therefore not limited to perennially frozen areas. Here, we review the latest approaches and methods for the study of plant aDNA from lake sediments and discuss the progress made up to the present. We argue that aDNA analyses add new and additional perspectives for the study of ancient plant populations and, in time, will provide higher taxonomic resolution and more precise estimation of abundance. Despite this, key questions and challenges remain for such plant aDNA studies. Finally, we provide guidelines on technical issues, including lake selection, and we suggest directions for future research on plant aDNA studies in lake sediments.
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Benthic algal assessment of ecological status in European lakes and rivers: Challenges and opportunities.
Poikane, S, Kelly, M, Cantonati, M
The Science of the total environment. 2016;:603-613
Abstract
This opinion paper introduces a special series of articles dedicated to freshwater benthic algae and their use in assessment and monitoring. This special series was inspired by talks presented at the 9th International Congress on the Use of Algae for Monitoring Rivers and Comparable Habitats (Trento, Italy, 2015), the latest of a series of meetings started in 1991. In this paper, we will first provide a brief overview of phytobenthos methods in Europe. Then, we will turn towards the 'dark side' of phytobenthos and describe four particular problems for phytobenthos assessment in the European Union: (1) over-reliance on a single group of algae (mostly diatoms) to the exclusion of other groups; (2) relatively low adoption of benthic algae for ecological assessments in lakes; (3) absence of measures of phytobenthos abundance; (4) approaches used to define boundaries between ecological classes. Following this, we evaluate the strengths and limitations of current phytobenthos assessment methods against 12 criteria for method evaluation addressing four areas: ecological rationale, performance, feasibility of implementation, and use in communication and management. Using these criteria, we identify and discuss three general challenges for those developing new methods for phytobenthos-based assessment: a weak ecological rationale and insufficient consideration of the role of phytobenthos as a diagnostic tool and for communicating ecosystem health beyond a narrow group of specialists. The papers in the special series allow a comparison with the situation and approaches in the USA, present new methods for the assessment of ecological status and acidification, provide tools for an improved management of headwaters and petrifying springs, discuss the utility of phytobenthos for lake assessments, and test the utility of functional measures (such as biofilm phosphorus uptake capacity, PUC).
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Effects of sediment geochemical properties on heavy metal bioavailability.
Zhang, C, Yu, ZG, Zeng, GM, Jiang, M, Yang, ZZ, Cui, F, Zhu, MY, Shen, LQ, Hu, L
Environment international. 2014;:270-81
Abstract
As the largest container and resource of metals, sediment has a special role in the fate of metals. Factors influencing bioavailability of heavy metals in sediment have never been comprehensively considered and the sediment properties still fail to understand and even controversial. In this review, the mechanisms of sediment properties such as acid-volatile sulfides (AVS), organic matter, texture (clay, silt or sand) and geology, organism behaviors as well as those influencing the bioavailability of metals were analyzed. Under anoxic condition, AVS mainly reduce the solubility and toxicity of metals, while organic matters, Fe-Mn oxides, clay or silt can stabilize heavy metals in elevated oxidative-reductive potential (ORP). Other factors including the variation of pH, redox potential, aging as well as nutrition and the behavior of benthic organism in sediment also largely alter metals mobility and distribution. These factors are often inter-related, and various toxicity assessment methods used to evaluate the bioavailability of trace metals have been also discussed. Additionally, we expect that some novel synthetic materials like polysulfides, nano-materials, provide the substantial amendments for metals pollution in sediment.
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Functional gene surveys from ocean drilling expeditions - a review and perspective.
Lever, MA
FEMS microbiology ecology. 2013;(1):1-23
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Abstract
The vast majority of microbes inhabiting the subseafloor remain uncultivated and their energy sources unknown. Thus, a focus of ocean drilling expeditions over the past decade has been to characterize the distribution of microbes associated with specific metabolic reactions. An important question has been whether microbes involved in key microbial processes, such as sulfate reduction and methanogenesis, differ fundamentally from their counterparts in surface environments. To this end, functional genes of anaerobic methane cycling (mcrA), sulfate reduction (dsrAB), acetogenesis (fhs), and dehalorespiration (rdhA) have been examined. A compilation of existing functional gene data suggests that subseafloor microbes involved in anaerobic methane cycling, sulfate reduction, acetogenesis, and dehalorespiration are not fundamentally different from their counterparts in the surface world. Moreover, quantifications of mcrA and dsrAB suggest that, unless the majority of subseafloor microbes involved in methane cycling and sulfate reduction are too genetically divergent to be detected with conventional methods, these processes only support a small fraction (< 1%) of total microbial biomass in the deep biosphere. Ecological explanations for the observed trends, target processes and methods for future investigations, and strategies for tackling the unresolved issue of microbial contamination in samples obtained by ocean drilling are discussed.
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Identification and characterization of ecologically significant prokaryotes in the sediment of freshwater lakes: molecular and cultivation studies.
Spring, S, Schulze, R, Overmann, J, Schleifer, K
FEMS microbiology reviews. 2000;(5):573-90
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Abstract
The aim of this review is to interpret recent studies in which molecular methods were used to identify and characterize prokaryotes in lake sediments and related habitats. In the first part studies based on the phylogenetic diversity of prokaryotes found in lacustrine habitats are summarized. The application of various cultivation-independent methods for the characterization of distinct groups of sediment bacteria is exemplified with morphologically conspicuous, colorless sulfur bacteria in the second part of this review. Finally, traditional and recently developed methods are described which could be used for linking the function of microbial populations with their identification. The potential of these approaches for the study of lake sediments is discussed in order to give a perspective for future studies in this habitat.