Biogeochemical cycling and microbial diversity in the thrombolitic microbialites of Highborne Cay,Bahamas

Thrombolites are unlaminated carbonate build‐ups that are formed via the metabolic activities of complex microbial mat communities. The thrombolitic mats of Highborne Cay, Bahamas develop in close proximity (1–2 m) to accreting laminated stromatolites, providing an ideal opportunity for biogeochemical and molecular comparisons of these two distinctive microbialite ecosystems. In this study, we provide the first comprehensive characterization of the biogeochemical activities and microbial diversity of the Highborne Cay thrombolitic mats. Morphological and molecular analyses reveal two dominant mat types associated with the thrombolite deposits, both of which are dominated by bacteria from the taxa Cyanobacteria and Alphaproteobacteria. Diel cycling of dissolved oxygen (DO) and dissolved inorganic carbon (DIC) were measured in all thrombolitic mat types. DO production varied between thrombolitic types and one morphotype, referred to in this study as ‘button mats’, produced the highest levels among all mat types, including the adjacent stromatolites. Characterization of thrombolite bacterial communities revealed a high bacterial diversity, roughly equivalent to that of the nearby stromatolites, and a low eukaryotic diversity. Extensive phylogenetic overlap between thrombolitic and stromatolitic microbial communities was observed, although thrombolite‐specific cyanobacterial populations were detected. In particular, the button mats were dominated by a calcified, filamentous cyanobacterium identified via morphology and 16S rRNA gene sequencing as Dichothrix sp. The distinctive microbial communities and chemical cycling patterns within the thrombolitic mats provide novel insight into the biogeochemical processes related to the lithifying mats in this system, and provide data relevant to understanding microbially induced carbonate biomineralization.     

Hydrodynamic disturbance controls microbial community assembly and biogeochemical processes in coastal sediments

The microbial community composition and biogeochemical dynamics of coastal permeable (sand) sediments differs from cohesive (mud) sediments. Tide- and wave-driven hydrodynamic disturbance causes spatiotemporal variations in oxygen levels, which select for microbial generalists and disrupt redox cascades. In this work, we profiled microbial communities and biogeochemical dynamics in sediment profiles from three sites varying in their exposure to hydrodynamic disturbance. Strong variations in sediment geochemistry, biogeochemical activities, and microbial abundance, composition, and capabilities were observed between the sites. Most of these variations, except for microbial abundance and diversity, significantly correlated with the relative disturbance level of each sample. In line with previous findings, metabolically flexible habitat generalists (e.g., Flavobacteriaceae, Woeseaiceae, Rhodobacteraceae) dominated in all samples. However, we present evidence that aerobic specialists such as ammonia-oxidizing archaea (Nitrosopumilaceae) were more abundant and active in more disturbed samples, whereas bacteria capable of sulfate reduction (e.g., uncultured Desulfobacterales), dissimilatory nitrate reduction to ammonium (DNRA; e.g., Ignavibacteriaceae), and sulfide-dependent chemolithoautotrophy (e.g., Sulfurovaceae) were enriched and active in less disturbed samples. These findings are supported by insights from nine deeply sequenced metagenomes and 169 derived metagenome-assembled genomes. Altogether, these findings suggest that hydrodynamic disturbance is a critical factor controlling microbial community assembly and biogeochemical processes in coastal sediments. Moreover, they strengthen our understanding of the relationships between microbial composition and biogeochemical processes in these unique environments.Subject terms: Water microbiology, Biogeochemistry     

PCR-DGGE技术用于湖泊沉积物中微生物群落结构多样性研究

采用PCR-DGGE分子指纹图谱技术比较南京市玄武湖、奠愁湖和太湖不同位置的表层沉积物微生物群落结构,研究结果表明,三湖泊沉积物微生物的16SrDNA的PCR扩增结果约为626bp,为16S rDNA V3～V5区特异性片段。玄武湖和莫愁湖表层沉积物中大约有20种优势菌群,且同一湖泊不同采样点DGGE图谱的差异性不大,细菌群落结构具有较高的相似性,而太湖样品DGGE条带的数目和位置表现出明显差异,且不同采样点图谱的差异性较大。三湖泊除具有特征性的微生物种属外,还分布约5个相同的细菌种群,可能与沉积物的理化性质和水生植被的影响相关。对DGGE图谱中7条主带进行回收、扩增和测序,结果显示其优势菌群具有不同的序列组成,其中5个序列与Genebank中已登录的细菌种群的同源性≥99％,2个序列的同源性为96％和93％,其中2个相似的细菌类群目前尚未获得纯培养。     

Biogeochemical transformations of arsenic in circumneutral freshwater sediments

Arsenic is a wide-spread contaminant of soils and sediments, andmany watersheds worldwide regularly experience severe arsenic loading. While the toxicityof arsenic to plants and animals is well recognized, the geochemical and biological transformationsthat alter its bioavailability in the environment are multifaceted and remain poorly understood.This communication provides a brief overview of our current understanding of the biogeochemistryof arsenic in circumneutral freshwater sediments, placing special emphasis on microbialtransformations. Arsenic can reside in a number of oxidation states and complex ions. The commoninorganic aqueous species at circumneutral pH are the negatively charged arsenates(H₂As^VO₄ ^- and Has^VO₄ ^2-) and zero-charged arsenite(H₃As^IIIO₃ ⁰). Arsenic undergoes diagenesis in response to both physicaland biogeochemical processes. It accumulates in oxic sediments by adsorption on and/orco-precipitation with hydrous iron and manganese oxides. Burial of such sediments in anoxic/suboxicenvironments favors their reduction, releasing Fe(II), Mn(II) and associatedadsorbed/coprecipitated As. Upward advection can translocate these cations and As into theoverlying oxic zone where they may reprecipitate. Alternatively, As may be repartitioned tothe sulfidic phase, forming precipitates such as arsenopyrite and orpiment. Soluble and adsorbedAs species undergo biotic transformations. As(V) can serve as the terminal electronacceptor in the biological oxidation of organic matter, and the limited number of microbes capableof this transformations are diverse in their phylogeny and physiology. Fe(III)-respiring bacteriacan mobilize both As(V) and As(III) bound to ferric oxides by the reductive dissolution ofiron-arsenate minerals. SO₄ ^2--reducing bacteria canpromote deposition of As(III) as sulfide minerals via their production of sulfide. A limited number of As(III)-oxidizing bacteriahave been identified, some of which couple this reaction to growth. Lastly, prokaryotic andeukaryotic microbes can alter arsenic toxicity either by coupling cellular export to its reductionor by converting inorganic As to organo-arsenical compounds. The degree to which each ofthese metabolic transformations influences As mobilization or sequestration in differentsedimentary matrices remains to be established.     

Biogeochemical influence on carbon isotope signature in boreal lake sediments

The functional morphology of the feeding palps and prostomium of the spionid polychaetes Streblospio benedicti and S. shrubsolii was studied. Three functional groups of cilia of the feeding palps were found on both species – frontal cilia, latero-frontal cirri and lateral cilia. Frontal cilia line the food groove and transport food particles to the pharynx, and have been reported for all spionid polychaetes except species of the genus Scolelepis. Latero-frontal cirri deflect particles onto the frontal surface and have been observed in several spionid genera including Paraprionospio, Streblospio, Polydora and Dipolydora. Lateral cilia beat in continuous metachronal waves creating lateral vortices that potentially entrain suspended particles, and are known in Paraprionospio and Streblospio. The two species of Streblospio did differ in the distribution of prostomial papillae. These papillae are eversible and thought to function in particle selection as particles on the pharynx come in contact with the papillae. Prostomial papillae were restricted to the peripheral surface of S. benedicti and were widely scattered on all surfaces of the prostomium of S. shrubsolii. A conical tentaculate structure occurs between the branchiae of the first setiger of S. benedicti, but only a low raised elevation is present on S. shrubsolii.     

Sedimentary context controls the influence of ecosystem engineering by bioturbators on microbial processes in river sediments

By modifying the physical environment, ecosystem engineers can have inordinately large effects on surrounding communities and ecosystem functioning. However, the significance of engineering in ecosystems greatly depends on the physical characteristics of the engineered habitats. Mechanisms underlying such context‐dependent impact of engineers remain poorly understood even though they are crucial to establish general predictions concerning the contribution of engineers to ecosystem structure and function. The present study aimed to decrypt such mechanisms by determining how the environmental context modulates the effects of ecosystem engineers (bioturbators) on microorganisms in river sediments. To test the effects of environmental context on the role of bioturbators in sediments, we used mesocosms and recreated two sedimentary contexts in the laboratory by adding a layer of either fine or coarse sand at the top of a gravel‐sand matrix. For each sediment context, we examined how the sediment reworking activity of a bioturbating tubificid worm (Tubifex tubifex) generated changes in the physical (sediment structure and permeability) and abiotic environments (hydraulic discharge, water chemistry) of microorganisms. Microbial characteristics (abundances, activities) and leaf litter decomposition – a major microbially‐mediated ecological process – were measured to evaluate the impact of bioturbation on biotic compartment. Our results showed that the permeability, the availability of oxygen and the activities of microorganisms were reduced in sediments covered with fine sand, in comparison with sediments covered with coarse sand. Tubifex tubifex significantly increased permeability (by about six‐fold), restored aerobic conditions and ultimately stimulated microbial communities (resulting in a 30% increase in leaf litter breakdown rate) in sediments covered with fine sand. In contrast T. tubifex had low effects in sediments topped by coarse sand, where O₂ was already available for hyporheic microorganisms. Our study supports the idea that context dependency mainly modulates the effects of engineering by controlling the ability of engineers to create changes on abiotic (O₂ in the present study) factors that are limiting for surrounding communities.     

Assessing microbial diversity using recent lake sediments and estimations of spatio‐temporal diversity

Aim Recent papers have used large palaeolimnological datasets to reveal the biodiversity patterns of aquatic microorganisms. However, scant attention has been paid to the influence of time on these patterns. Where lake surficial sediment samples are used as integrals of diversity, the time interval of each sample varies according to differences in sediment accumulation rates. This paper aims to test the reliability of using lake surface sediments to measure and to compare microbial diversity when the potential influences of the species–time relationships are taken into account. Location Alpine lakes in Europe. Methods We analysed microorganism (siliceous microalgae) assemblages in three European Alpine lakes using short sediment cores (²¹⁰Pb‐dated) and annual sediment trap samples from 12 UK lakes. The same number of individuals was pooled for each sample 500 times to avoid sampling effort effects and to standardize species diversity estimation. The influence of time on the diversity score was assessed by simulating an increase of time span for surface sediment samples by cumulatively adding in successive sediment core samples (from the most recent to the oldest). We used species richness (S) and the exponential of the bias‐corrected Shannon entropy index (exp(H_b‐c)) to estimate diversity. Results Increasing the time interval represented by a surficial sediment sample did not affect the diversity results. The estimation of diversity was similar for cumulative and non‐cumulative samples. Diversity estimation was only altered in lakes experiencing high community turnover due to strong environmental forcing during the time period spanned by the cumulative sample. Main conclusions The use of surface lake sediments is suitable for estimating the average site diversity of free‐living microorganisms. Diversity is integrated in a single sample and species assemblage composition is derived from microbial communities living in distinct lake microhabitats. Species remains, accumulated in a single sample over several years of environmental variability, represent a diversity integral that captures a spatio‐temporal component equivalent to the γ‐diversity measure.     

Impact of mariculture on microbial diversity in sediments near open ocean farming of Polydactylus sexfilis

A chemical and microbiological investigation was performed to determine ecological impact in sediments below a new offshore mariculture operation on the southwest coast of Oahu, Hawaii. Sediment samples collected directly below the fish enclosures were compared with sediment collected 300 m upcurrent. Total organic carbon was 25–37% higher in the control compared with cage samples and ammonia was 30–46% higher in cage samples. Sulfate reducing bacteria (SRB) counts were 36% higher in cage sample sediments.Genomic 16S rDNA was PCR amplified from total DNA extracted from sediments and analyzed by denaturing gradient gel electrophoresis (DGGE). Similar gradient profiles for control and cage samples were observed. Cloned 16S rDNA libraries for species sampling and determination indicate similar and diverse bacterial communities. Bacteria belonging to the γ-Proteobacteria class were frequently represented and atypical or pathogenic bacterial species were not detected.A mathematical model developed for prediction of organic material deposition suggests that while currents will reduce fecal loading and feed deposition beneath a cage, there is expected to be sufficient nutrient addition to impact those sediments. Time series or statistical information on the current field beneath the fish cages are needed to apply the model for predicting locations of high deposition. This would contribute to the development of a comprehensive monitoring program that would sample multiple locations over time to generate an accurate and comprehensive depiction of the environmental impacts of this new and expanding commercial endeavor.     

Quinone profiles in lake sediments: Implications for microbial diversity and community structures

Microbial quinone compositions of sediment mud samples from five different lakes in Japan were studied by spectrochromatography and mass spectrometry. The total quinone content of these samples ranged from 1.97 to 18.0 nmol/g dry weight of sediment, of which a combined fraction of ubiquinones and menaquinones accounted for 42 to 74%. The remaining fraction (26 to 58%) consisted of the photosynthetic quinones, plastoquinones and phylloquinone. The sediment samples produced PQ-9 or Q-8 as the most abundant quinone type regardless of their geographic locations and depths. These results indicate that oxygenic phototrophic microorganisms and Q-8-containing proteobacteria constituted major parts of microbial populations in the lake sediment. In the surface water of the same sampling sites, plastoquinones and phylloquinone occurred in much higher proportions. These findings suggested that the high abundance of oxygenic phototrophs in the sediment muds resulted from their constant movement or sedimentation from the surface water. Numerical analyses of the quinone profiles showed that the microbial communities of the sediment were diverse and different in different lakes but similar to each other in the diversity of bioenergetic modes. Three physiological groups of microbes showing ubiquinone-mediated aerobic respiration, oxygenic photosynthesis, and menaquinone-associated respiration were suggested to inhabit the lake sediments in balance.     

Rates and controls of anaerobic microbial respiration across spatial and temporal gradients in saltmarsh sediments

This study was undertaken to determine the rates and controls ofanaerobic respiration reactions coupled to organic matter mineralization as afunction of space and time along a transect from a bioturbated creekbank to themidmarsh in Georgia saltmarsh sediments. Sulfate reduction rates (SRR) weremeasured at 3 sites during 5 sampling periods throughout the growth season. Thesites differed according to hydrologic regime and the abundance of dominantplants and macrofauna. SRR and pore water / solid phase geochemistry showedevidence of enhanced sediment oxidation at sites exposed to intensebioturbation. Iron(III) reduction rates (FeRR) were directly determined insaltmarsh sediments for the first time, and in agreement with measured SRR,higher rates were observed at the bioturbated, unvegetated creekbank (BUC) andbioturbated, vegetated levee (BVL) sites in comparison to a vegetated mid-marsh(MM) site. An unexpected result was the fact that SRR varied nearly as muchbetween sites (2–3 x) as it did with temperature or season (3–4 x).The BVL site, vegetated by the tall form of Spartinaalterniflora, always exhibited the highest SRR and carbon oxidationrates (> 4000 nmol cm^–3 d^–1) with high activity levels extending deep ( 50 cm)into the sediment, while the MM site, dominated by the short form ofSpartina, always exhibited the lowest SRR which werelocalized to the top 15 cm of sediment. SRR and FeRR at BUC wereintermediate between those measured at the BVL and MM. Acetate was the mostabundant microbial fermentation product (concentrations up to > 1mM) in marsh porewaters, and its distribution reflectedrespirationactivity. Chemical exchange, caused by bioturbation, appeared to be the primarycontrol explaining trends in rates of sulfate and Fe(III) reduction withmacrophytes and carbon source acting as secondary controls.     

Microbial diversity and activity in seafloor brine lake sediments (Alaminos Canyon block 601, Gulf of Mexico)

The microbial communities thriving in deep‐sea brines are sustained largely by energy rich substrates supplied through active seepage. Geochemical, microbial activity, and microbial community composition data from different habitats at a Gulf of Mexico brine lake in Alaminos Canyon revealed habitat‐linked variability in geochemistry that in turn drove patterns in microbial community composition and activity. The bottom of the brine lake was the most geochemically extreme (highest salinity and nutrient concentrations) habitat and its microbial community exhibited the highest diversity and richness indices. The habitat at the upper halocline of the lake hosted the highest rates of sulfate reduction and methane oxidation, and the largest inventories of dissolved inorganic carbon, particulate organic carbon, and hydrogen sulfide. Statistical analyses indicated a significant positive correlation between the bacterial and archaeal diversity in the bottom brine sample and inventories. Other environmental factors with positive correlation with microbial diversity indices were DOC, H₂S, and DIC concentrations. The geochemical regime of different sites within this deep seafloor extreme environment exerts a clear selective force on microbial communities and on patterns of microbial activity.     

Comparison of the microbial diversity in cold-seep sediments from different depths in the Nankai Trough

We have investigated the molecular phylogeny of cold-seep sediments obtained from the Nankai Trough, at depths of about 600, 2,000, and 3,300 m, and compared the microbial diversity profiles of those sediments samples. The gamma-Proteobacteria that might function as sulfide oxidizers and the symbiotically related delta-Proteobacteria which might function as sulfate reducers were identified amongst the bacteria from all depths of the sediments. However, anoxic methane oxidizing archaea (ANME) and methanogens were only found in the 600 m deep sediments. These results indicated that the cold-seep microbial sulfur circulation system could be functioning in the shallow seep sediment at a depth of 600 m and the microbial activities at these sites might be more dynamic than at other deeper cold-seep sites.     

Seasonal and spatial diversity of microbial communities in marine sediments of the South China Sea

This study was conducted to characterize the diversity of microbial communities in marine sediments of the South China Sea by means of 16S rRNA gene clone libraries. The results revealed that the sediment samples collected in summer harboured a more diverse microbial community than that collected in winter, Deltaproteobacteria dominated 16S rRNA gene clone libraries from both seasons, followed by Gammaproteobacteria, Acidobacteria, Nitrospirae, Planctomycetes, Firmicutes. Archaea phylotypes were also found. The majority of clone sequences shared greatest similarity to uncultured organisms, mainly from hydrothermal sediments and cold seep sediments. In addition, the sedimentary microbial communities in the coastal sea appears to be much more diverse than that of the open sea. A spatial pattern in the sediment samples was observed that the sediment samples collected from the coastal sea and the open sea clustered separately, a novel microbial community dominated the open sea. The data indicate that changes in environmental conditions are accompanied by significant variations in diversity of microbial communities at the South China Sea.     

Biogeochemical and physical controls on methane fluxes from two ferruginous meromictic lakes

Meromictic lakes with anoxic bottom waters often have active methane cycles whereby methane is generally produced biogenically under anoxic conditions and oxidized in oxic surface waters prior to reaching the atmosphere. Lakes that contain dissolved ferrous iron in their deep waters (i.e., ferruginous) are rare, but valuable, as geochemical analogues of the conditions that dominated the Earth's oceans during the Precambrian when interactions between the iron and methane cycles could have shaped the greenhouse regulation of the planet's climate. Here, we explored controls on the methane fluxes from Brownie Lake and Canyon Lake, two ferruginous meromictic lakes that contain similar concentrations (max. >1 mM) of dissolved methane in their bottom waters. The order Methanobacteriales was the dominant methanogen detected in both lakes. At Brownie Lake, methanogen abundance, an increase in methane concentration with respect to depths closer to the sediment, and isotopic data suggest methanogenesis is an active process in the anoxic water column. At Canyon Lake, methanogenesis occurred primarily in the sediment. The most abundant aerobic methane‐oxidizing bacteria present in both water columns were associated with the Gammaproteobacteria, with little evidence of anaerobic methane oxidizing organisms being present or active. Direct measurements at the surface revealed a methane flux from Brownie Lake that was two orders of magnitude greater than the flux from Canyon Lake. Comparison of measured versus calculated turbulent diffusive fluxes indicates that most of the methane flux at Brownie Lake was non‐diffusive. Although the turbulent diffusive methane flux at Canyon Lake was attenuated by methane oxidizing bacteria, dissolved methane was detected in the epilimnion, suggestive of lateral transport of methane from littoral sediments. These results highlight the importance of direct measurements in estimating the total methane flux from water columns, and that non‐diffusive transport of methane may be important to consider from other ferruginous systems.     

Phylogenetic diversity of microbial communities of the Posolsk Bank bottom sediments,Lake Baikal

Massive parallel sequencing (the Roche 454 platform) of the 16S rRNA gene fragments was used to investigate microbial diversity in the sediments of the Posolsk Bank cold methane seep. Bacterial communities from all sediment horizons were found to contain members of the phyla Actinobacteria, Bacteroidetes, Deinococcus-Thermus, Firmicutes, Nitrospirae, Chloroflexi, Proteobacteria, and the candidate phyla Aminicenantes (OP8) and Atribacteria (OP9). Among Bacteria, members of the Chloroflexi and Proteobacteria were the most numerous (42 and 46%, respectively). Among archaea, the Thaumarchaeota predominated in the upper sediment layer (40.1%), while Bathyarchaeota (54.2%) and Euryarchaeota (95%) were predominant at 70 and 140 cm, respectively. Specific migration pathways of fluid flows circulating in the zone of gas hydrate stability (400 m) may be responsible for considerable numbers of the sequences of Chloroflexi, Acidobacteria, and the candidate phyla Aminicenantes and Atribacteria in the upper sediment layers and of the Deinococcus-Thermus phylum in deep bottom sediments.     

Biogeochemical and hydrological controls on carbon export from a forested catchment in central Japan

Here we review research on the links between hydrological processes and the biogeochemical environment controlling the dynamics of dissolved organic carbon (DOC) and dissolved inorganic carbon (DIC) in temperate forested catchments. In addition, we present the results of original experiments. The spatial and temporal changes in DIC and DOC concentrations were investigated in tandem with observations of elementary belowground hydrological processes for a forested headwater catchment in central Japan. The soil CO₂ gas concentration, which is the source of DIC, increased with depth. The hydrological characteristics of groundwater also affected the spatial variation of partial pressure of dissolved CO₂ (pCO₂) in groundwater. The temporal variations in the soil CO₂ gas concentration and the pCO₂ values of groundwater suggested that the dynamics of DIC were strongly affected by biological activity. However, the geographical differences in DIC leaching were affected not only by the link between climatological conditions and biological activity, but also by other factors such as geomorphologic conditions. The DOC concentrations decreased with selective removal of hydrophobic acid during vertical infiltration. The major DOC-removal mechanisms were retention of metal-organic complexes to soil solids in the upper mineral soil layer and decomposition of DOC in the lower mineral soil layer. The responses of the DIC and DOC concentrations to changes in discharge during storm events were explained by the spatial variation in the DIC and DOC concentrations. Seasonal variation, which represents a long-term change, in stream water DOC concentrations was affected not only by the temporal variation in DOC concentrations in the topsoil, which may be affected by biological activity, but also by water movement, which transports DOC from the topsoil to stream water. These results indicate that both a biogeochemical approach and a method for evaluating the hydrological effects on carbon dynamics are critical for clarifying the carbon accumulation-and-release processes in forested ecosystems.     

Genome diversity in microbial eukaryotes

The genomic peculiarities among microbial eukaryotes challenge the conventional wisdom of genome evolution. Currently, many studies and textbooks explore principles of genome evolution from a limited number of eukaryotic lineages, focusing often on only a few representative species of plants, animals and fungi. Increasing emphasis on studies of genomes in microbial eukaryotes has and will continue to uncover features that are either not present in the representative species (e.g. hypervariable karyotypes or highly fragmented mitochondrial genomes) or are exaggerated in microbial groups (e.g. chromosomal processing between germline and somatic nuclei). Data for microbial eukaryotes have emerged from recent genome sequencing projects, enabling comparisons of the genomes from diverse lineages across the eukaryotic phylogenetic tree. Some of these features, including amplified rDNAs, subtelomeric rDNAs and reduced genomes, appear to have evolved multiple times within eukaryotes, whereas other features, such as absolute strand polarity, are found only within single lineages.     

Anaerobic microbial methanol conversion in marine sediments

Methanol is an ubiquitous compound that plays a role in microbial processes as a carbon and energy source, intermediate in metabolic processes or as end product in fermentation. In anoxic environments, methanol can act as the sole carbon and energy source for several guilds of microorganisms: sulfate-reducing microorganisms, nitrate-reducing microorganisms, acetogens and methanogens. In marine sediments, these guilds compete for methanol as their common substrate, employing different biochemical pathways. In this review, we will give an overview of current knowledge of the various ways in which methanol reaches marine sediments, the ecology of microorganisms capable of utilizing methanol and their metabolism. Furthermore, through a metagenomic analysis, we shed light on the unknown diversity of methanol utilizers in marine sediments which is yet to be explored.