Speleothems from Sahastradhara Caves in Siwalik Himalaya,India: Possible Biogenic Inputs

Stalactites and moonmilk from Sahastradhara caves in Siwalik Himalayas were studied to understand the role of microbes in their genesis. Fourier spectroscopy in the moonmilk indicates a complex milieu of organic compounds that is unusual for inorganic formations. Stable C and O isotopes show trends in the moonmilk and stalactite, which suggest biogenic input; the geochemical inference is consistent with evidence from microscopy and laboratory-based microbial cultures. Light microscopy of moonmilk samples show the presence of a number of microbial forms similar to Cyanobacteria, and scanning electron microscope (SEM) images show microbial structures similar to Spirulina. The total number of microbial cells using SYBR Gold is 6.5 × 10⁵ cells, g sed^?1in moonmilk and 3.2 × 10⁵ cells, g sed^?1 in stalactites. FISH indicates approximately 3.5 × 10⁵ cells, g sed^?1 in moonmilk and 2 × 10⁵ cells, g sed^?1 in stalactites. SEM images of the moonmilk indicate a large network of microbial filaments along with minerals, which are identified as calcite based on their x-ray diffraction pattern. In vitro laboratory cultures with pure monogenic strains isolated from the moonmilk and stalactites raise pH in the medium, which facilitate calcite precipitation. The mineral precipitating isolates were identified as: Bacillus pumilis, B. cereus, B. anthracis, B. lentus, B. sphaericus, B. circulans and Actinomycetes. The Sahastradhara moonmilk and statactites are colonized by a diverse microbial community and the isolated bacterial strains induce biomineralization on different nutrient media, supporting their biogenic origin.     

A mineralogical characterization of biogenic calcium carbonates precipitated by heterotrophic bacteria isolated from cryophilic polar regions

Precipitation of calcium carbonate (CaCO_3(s)) can be driven by microbial activity. Here, a systematic approach is used to identify the morphological and mineralogical characteristics of CaCO_3(s) precipitated during the heterotrophic growth of micro‐organisms isolated from polar environments. Focus was placed on establishing mineralogical features that are common in bioliths formed during heterotrophic activity, while in parallel identifying features that are specific to bioliths precipitated by certain microbial phylotypes. Twenty microbial isolates that precipitated macroscopic CaCO_3(s) when grown on B4 media supplemented with calcium acetate or calcium citrate were identified. A multimethod approach, including scanning electron microscopy, high‐resolution transmission electron microscopy, and micro‐X‐ray diffraction (μ‐XRD), was used to characterize CaCO_3(s) precipitates. Scanning and transmission electron microscopy showed that complete CaCO_3(s) crystal encrustation of Arthrobacter sp. cells was common, while encrustation of Rhodococcus sp. cells did not occur. Several euhedral and anhedral mineral formations including disphenoid‐like epitaxial plates, rhomboid‐like aggregates with epitaxial rhombs, and spherulite aggregates were observed. While phylotype could not be linked to specific mineral formations, isolates tended to precipitate either euhedral or anhedral minerals, but not both. Three anhydrous CaCO_3(s) polymorphs (calcite, aragonite, and vaterite) were identified by μ‐XRD, and calcite and aragonite were also identified based on TEM lattice‐fringe d value measurements. The presence of certain polymorphs was not indicative of biogenic origin, although several mineralogical features such as crystal‐encrusted bacterial cells, or casts of bacterial cells embedded in mesocrystals are an indication of biogenic origin. In addition, some features such as the formation of vaterite and bacterial entombment appear to be linked to certain phylotypes. Identifying phylotypes consistent with certain mineralogical features is the first step toward discovering a link between these crystal features and the precise underlying molecular biology of the organism precipitating them.     

Biogenic Evidences of Moonmilk Deposition in the Mawmluh Cave,Meghalaya, India

Moonmilk, a microcrystalline secondary cave deposit, actively forms on the floor of Krem Mawmluh – a limestone cave in Meghalaya, Northeastern India. Due to the abundance of micrite and calcified microbial filaments, we hypothesize that these deposits form as a result of ongoing microbial interactions. Consistent with this idea, we report electron microscopic and microbiological evidences for the biological origin of moonmilk in Krem Mawmluh. Scanning electron microscopy indicated abundant calcified microbial filaments, needle calcite, fibre calcites (micro-fibre and nano-fibre calcite crystals), biofilm and microbial filaments in the moonmilk. The total viable culturable microbes showed high population densities for microbes in the moonmilk and moonmilk pool waters. In vitro culture experiments, confirmed the capability of many of the isolated strains to precipitate calcite and some of the identified isolates belonged to the Bacillus sp. and Actinomycetes. These results clearly support the biogenic nature of the deposits.     

Interaction between lithification and resource availability in the microbialites of Río Mesquites,Cuatro Ciénegas,México

Lithified microbial structures (microbialites) have been present on Earth for billions of years. Lithification may impose unique constraints on microbes. For instance, when CaCO₃ forms, phosphate may be captured via coprecipitation and/or adsorption and potentially rendered unavailable for biological uptake. Therefore, the growth of microbes associated with CaCO₃ may be phosphorus‐limited. In this study, we compared the effects of resource addition on biogeochemical functions of microbial communities associated with microbialites and photoautotrophic microbial communities not associated with CaCO₃ deposition in Río Mesquites, Cuatro Ciénegas, México. We also manipulated rates of CaCO₃ deposition in microbialites to determine whether lithification reduces the bioavailability of phosphorus (P). We found that P additions significantly increased rates of gross primary production (F_2,13 = 103.9, P < 0.001), net primary production (F_2,13 = 129.6, P < 0.0001) and ecosystem respiration (F_2,13 = 6.44, P < 0.05) in the microbialites, while P addition had no effect on photoautotrophic production in the non‐CaCO₃‐associated microbial communities. Growth of the non‐CaCO₃‐associated phototrophs was only marginally stimulated when nitrogen and P were added simultaneously (F_1,36 = 3.98, P = 0.053). In the microbialites, resource additions led to some shifts in the abundance of Proteobacteria, Bacteroidetes and Cyanobacteria but mostly had little effect on bacterial community composition. Ca²⁺ uptake rates increased significantly with organic carbon additions (F_1,13 = 8.02, P < 0.05). Lowering of CaCO₃ deposition by decreasing calcium concentrations in the water led to increased microbial biomass accumulation rates in terms of both organic carbon (F_4,48 = 5.23, P < 0.01) and P (F_6,48 = 13.91, P < 0.001). These results provide strong evidence in support of a role of lithification in controlling P limitation of microbialite communities.     

Geomicrobial Processes and Biodiversity in the Deep Terrestrial Subsurface

The concept of a deep microbial biosphere has advanced over the past several decades from a hypothesis viewed with considerable skepticism to being widely accepted. Phylogenetically diverse prokaryotes have been cultured from or detected via characterization of directly-extracted nucleic acids from a wide range of deep terrestrial environments. Recent advances have linked the metabolic potential of these microorganisms, determined directly or inferred from phylogeny, to biogeochemical reactions determined via geochemical measurements and modeling. Buried organic matter or kerogen is an important source of energy for sustaining anaerobic heterotrophic microbial communities in deep sediments and sedimentary rock although rates of respiration are among the slowest rates measured on the planet. In contrast, Subsurface Lithoautotrophic Microbial Ecosystems based on H ₂ as the primary energy source appear to dominate in many crystalline rock environments. These photosynthesis-independent ecosystems remain an enigma due to the difficulty in accessing and characterizing appropriate samples. Deep mines and dedicated rock laboratories, however, may offer unprecedented opportunities for investigating subsurface microbial communities and their interactions with the geosphere.     

New Undescribed Lineages of Non-extremophilic Archaea Form a Homogeneous and Dominant Element Within Alpine Moonmilk Microbiomes

The moonmilk deposits within the alpine Hundsalm cave in Austria offered the opportunity to investigate anthropogenically uninfluenced microbiomes. Via cultivation experiments we were able to show that the communities were cold-adapted and oligotrophic. Combined qPCR, DGGE, cloning and sequencing data further highlighted that the archaeal community basically comprises a low number of species, though highly abundant. These organisms are assumed to form new lineages within the Euryarchaeota, while the detected Thaumarchaeota, closely related to ammonium oxidizers, form a second, but minor, abundant group within the moonmilk deposits. Moreover, in terms of abundance the archaeal community clearly outnumbers bacteria (e.g., genera Pseudomonas, Flavobacterium and Rhodococcus) and fungi within the investigated microbiomes. In contrast to the highly complex bacterial and fungal communities, only a low number of archaeal species form a constant and essential element within the moonmilk speleothems and other cave-internal habitats.     

Microbial Community Diversity of Moonmilk Deposits at Ballynamintra Cave, Co. Waterford, Ireland

Caves are extreme and specialised habitats for terrestrial life that sometimes contain moonmilk, a fine-grained paste-like secondary mineral deposit that is found in subterranean systems worldwide. While previous studies have investigated the possible role of microorganisms in moonmilk precipitation, the microbial community ecology of moonmilk deposits is poorly understood. Bacterial and fungal community structure associated with four spatially isolated microcrystalline, acicular calcite moonmilk deposits at Ballynamintra Cave (S. Ireland) was investigated during this study. Statistical analyses revealed significant differences in microbial activity, number of bacterial species, bacterial richness and diversity, and fungal diversity (Shannon's diversity) among the moonmilk sites over an area of approximately 2.5 m². However, the number of fungal species and fungal community richness were unaffected by sampling location. SIMPER analysis revealed significant differences in bacterial and fungal community composition among the sampling sites. These data suggest that a rich assemblage of microorganisms exists associated with moonmilk, with some spatial diversity, which may reflect small-scale spatial differences in cave biogeochemistry.     

Ecology of aquatic Ranunculus communities under the Mediterranean climate

The Iberian Peninsula encompasses more than 80% of the species richness of European aquatic ranunculi. The floristic diversity of the phytocoenosis characterised by aquatic Ranunculus and the main physical–chemical factors of the water were studied in 43 localities of the central Iberian Peninsula. Four aquatic Ranunculus communities are found in most of the aquatic environments. These are species-poor and have an uneven distribution: three species of Batrachium are heterophyllous and their communities are distributed in different aquatic ecosystems on silicated substrates; one species is homophyllous and its community occurs in various aquatic ecosystems with carbonated waters. In the Mediterranean climate, Ranunculus species are present in different habitats, as shown by the results of all the statistical analyses. Ranunculus trichophyllus communities occur in base-rich waters with a high buffering capacity (2273.44 ± 794.57 mg CaCO₃ L⁻¹) and a high concentration of cations (Ca²⁺, 121 ± 33.12 mg L⁻¹; Mg²⁺, 71.64 ± 82.77 mg L⁻¹), nitrates (2.89 ± 4.80 mg L⁻¹), ammonium (2.19 ± 1.36 mg L⁻¹) and sulphates (216.25 ± 218.54 mg L⁻¹). Ranunculus penicillatus communities are found in flowing waters with a high concentration of phosphates (0.48 ± 0.6 mg L⁻¹) and intermediate buffering capacity (683.66 ± 446.76 mg CaCO₃ L⁻¹). Both Ranunculus pseudofluitans and Ranunculus peltatus communities grow in waters with low buffering capacity (R. pseudofluitans, 385.91 ± 209.2 mg CaCO₃ L⁻¹; R. peltatus, 263.3 ± 180.36 mg CaCO₃ L⁻¹), and a low concentration of cations (R. pseudofluitans: Ca²⁺, 12.57 ± 9.42 mg L⁻¹; Mg²⁺, 3.42 ± 1.67 mg L⁻¹; R. peltatus: Ca²⁺, 15 ± 18.26 mg L⁻¹; Mg²⁺, 6.26 ± 8.89 mg L⁻¹) and nutrients (R. pseudofluitans: nitrates, 0.23 ± 0.2 mg L⁻¹; phosphates, 0.09 ± 0.1 mg L⁻¹; R. peltatus: nitrates, 0.19 ± 0.21 mg L⁻¹; phosphates, 0.09 ± 0.12 mg L⁻¹); the first in flowing waters, the latter in still waters.     

Microbial life associated with low‐temperature alteration of ultramafic rocks in the Leka ophiolite complex

Water–rock interactions in ultramafic lithosphere generate reduced chemical species such as hydrogen that can fuel subsurface microbial communities. Sampling of this environment is expensive and technically demanding. However, highly accessible, uplifted oceanic lithospheres emplaced onto continental margins (ophiolites) are potential model systems for studies of the subsurface biosphere in ultramafic rocks. Here, we describe a microbiological investigation of partially serpentinized dunite from the Leka ophiolite (Norway). We analysed samples of mineral coatings on subsurface fracture surfaces from different depths (10–160 cm) and groundwater from a 50‐m‐deep borehole that penetrates several major fracture zones in the rock. The samples are suggested to represent subsurface habitats ranging from highly anaerobic to aerobic conditions. Water from a surface pond was analysed for comparison. To explore the microbial diversity and to make assessments about potential metabolisms, the samples were analysed by microscopy, construction of small subunit ribosomal RNA gene clone libraries, culturing and quantitative‐PCR. Different microbial communities were observed in the groundwater, the fracture‐coating material and the surface water, indicating that distinct microbial ecosystems exist in the rock. Close relatives of hydrogen‐oxidizing Hydrogenophaga dominated (30% of the bacterial clones) in the oxic groundwater, indicating that microbial communities in ultramafic rocks at Leka could partially be driven by H₂ produced by low‐temperature water–rock reactions. Heterotrophic organisms, including close relatives of hydrocarbon degraders possibly feeding on products from Fischer–Tropsch‐type reactions, dominated in the fracture‐coating material. Putative hydrogen‐, ammonia‐, manganese‐ and iron‐oxidizers were also detected in fracture coatings and the groundwater. The microbial communities reflect the existence of different subsurface redox conditions generated by differences in fracture size and distribution, and mixing of fluids. The particularly dense microbial communities in the shallow fracture coatings seem to be fuelled by both photosynthesis and oxidation of reduced chemical species produced by water–rock reactions.     

Differential modification of seawater carbonate chemistry by major coral reef benthic communities

Ocean acidification (OA) resulting from uptake of anthropogenic CO₂ may negatively affect coral reefs by causing decreased rates of biogenic calcification and increased rates of CaCO₃ dissolution and bioerosion. However, in addition to the gradual decrease in seawater pH and Ω _a resulting from anthropogenic activities, seawater carbonate chemistry in these coastal ecosystems is also strongly influenced by the benthic metabolism which can either exacerbate or alleviate OA through net community calcification (NCC = calcification – CaCO₃ dissolution) and net community organic carbon production (NCP = primary production ? respiration). Therefore, to project OA on coral reefs, it is necessary to understand how different benthic communities modify the reef seawater carbonate chemistry. In this study, we used flow-through mesocosms to investigate the modification of seawater carbonate chemistry by benthic metabolism of five distinct reef communities [carbonate sand, crustose coralline algae (CCA), corals, fleshy algae, and a mixed community] under ambient and acidified conditions during summer and winter. The results showed that different communities had distinct influences on carbonate chemistry related to the relative importance of NCC and NCP. Sand, CCA, and corals exerted relatively small influences on seawater pH and Ω _a over diel cycles due to closely balanced NCC and NCP rates, whereas fleshy algae and mixed communities strongly elevated daytime pH and Ω _a due to high NCP rates. Interestingly, the influence on seawater pH at night was relatively small and quite similar across communities. NCC and NCP rates were not significantly affected by short-term acidification, but larger diel variability in pH was observed due to decreased seawater buffering capacity. Except for corals, increased net dissolution was observed at night for all communities under OA, partially buffering against nighttime acidification. Thus, algal-dominated areas of coral reefs and increased net CaCO₃ dissolution may partially counteract reductions in seawater pH associated with anthropogenic OA at the local scale.     

Biogenic Polyamines Capture CO2 and Accelerate Extracellular Bacterial CaCO3 Formation

Bacteria, including cyanobacteria, as well as some fungi, are known to deposit calcium carbonate (CaCO₃) extracellularly in calcium-containing artificial medium. Despite extensive investigation, the mechanisms involved in extracellular formation of CaCO₃ by bacteria have remained unclear. The ability of synthetic amines to remove carbon dioxide (CO₂) from natural gas led us to examine the role of biogenic polyamines in CaCO₃ deposition by bacteria. Here, we demonstrated that biogenic polyamines such as putrescine, spermidine, and spermine were able to react with atmospheric CO₂ and the resultant carbamate anion was characterized by using nuclear magnetic resonance (NMR) analysis. Biogenic polyamines accelerated the formation of CaCO₃, and we artificially synthesized the dumbbell-shaped calcites, which had the same form as observed with bacterial CaCO₃ precipitates, under nonbacterial conditions by using polyamines. The reaction rate of calcification increased with temperature with an optimum of around 40 °C. Our observation suggests a novel scheme for CO₂ dissipation that could be a potential tool in reducing atmospheric CO₂ levels and, therefore, global warming.     

Geological gas-storage shapes deep life

Around the world, several dozen deep sedimentary aquifers are being used for storage of natural gas. Ad hoc studies of the microbial ecology of some of them have suggested that sulfate reducing and methanogenic microorganisms play a key role in how these aquifers' communities function. Here, we investigate the influence of gas storage on these two metabolic groups by using high-throughput sequencing and show the importance of sulfate-reducing Desulfotomaculum and a new monophyletic methanogenic group. Aquifer microbial diversity was significantly related to the geological level. The distance to the stored natural gas affects the ratio of sulfate-reducing Firmicutes to deltaproteobacteria. In only one aquifer, the methanogenic archaea dominate the sulfate-reducers. This aquifer was used to store town gas (containing at least 50% H₂) around 50 years ago. The observed decrease of sulfates in this aquifer could be related to stimulation of subsurface sulfate-reducers. These results suggest that the composition of the microbial communities is impacted by decades old transient gas storage activity. The tremendous stability of these gas-impacted deep subsurface microbial ecosystems suggests that in situ biotic methanation projects in geological reservoirs may be sustainable over time.     

Exopolymeric substances of sulfate-reducing bacteria: Interactions with calcium at alkaline pH and implication for formation of carbonate minerals

Sulfate‐reducing bacteria (SRB) have been recognized as key players in the precipitation of calcium carbonate in lithifying microbial communities. These bacteria increase the alkalinity by reducing sulfate ions, and consuming organic acids. SRB also produce copious amounts of exopolymeric substances (EPS). All of these processes influence the morphology and mineralogy of the carbonate minerals. Interactions of EPS with metals, calcium in particular, are believed to be the main processes through which the extracellular matrix controls the precipitation of the carbonate minerals. SRB exopolymers were purified from lithifying mat and type cultures, and their potential role in CaCO₃ precipitation was determined from acid‐base titrations and calcium‐binding experiments. Major EPS characteristics were established using infrared spectroscopy and gas chromatography to characterize the chemical functional groups and the sugar monomers composition. Our results demonstrate that all of the three SRB strains tested were able to produce large amounts of EPS. This EPS exhibited three main buffering capacities, which correspond to carboxylic acids (pK_a = 3.0), sulfur‐containing groups (thiols, sulfonic and sulfinic acids – pK_a = 7.0–7.1) and amino groups (pK_a = 8.4–9.2). The calcium‐binding capacity of these exopolymers in solution at pH 9.0 ranged from 0.12g_Ca g_EPS^?1–0.15 g_Ca g_EPS^?1. These results suggest that SRB could play a critical role in the formation of CaCO₃ in lithifying microbial mats. The unusually high sulfur content, which has not been reported for EPS before, indicates a possible strong interaction with iron. In addition to changing the saturation index through metabolic activity, our results imply that SRB affect the rock record through EPS production and its effect on the CaCO₃ precipitation. Furthermore, EPS produced by SRB may account for the incorporation of metals (e.g. Sr, Fe, Mg) associated with carbonate minerals in the rock record.     

Effects of soil pH and calcium on mycorrhizas of Picea abies

The effects of lime, increased soil pH and increased soil Ca concentration on the mycorrhizas of Norway spruce. [Picea abies (L.) Karst.] were studied independently of each other to elucidate the different mechanisms through which lime may influence mycorrhizas in acidic soil. In a field experiment (mature Norway spruce in podzol), lime was applied as CaCO₃; increased Ca concentration without an increase in pH was achieved with CaSO₄; and soil pH was increased without calcium by means of Na₂CO₃ and K₂CO₃ (Na+K treatment). Treatments were done in October, and mycorrhizas were counted from samples collected in the following June and September. All treatments increased the percentage of dead short root tips compared to controls in September, and Na+K already in June. Cenococcum geophilum Fr. increased in proportion in plots treated with Na+K.In a sand culture experiment, Norway spruce seedlings were grown from seed and inoculated with Cenococcum geophilum, or root inoculum, or left uninoculated. When mycorrhizas were beginning to form, CaCO₃ and CaSO₄ treatments were applied. Six weeks later, the percent of dead short root tips in both salt treatments was significantly increased from control, but formation of mycorrhizas was not inhibited by treatments.As all the treatments increased the proportion of dead short root tips, it is concluded that lime directly and adversely affected mycorrhizas of Norway spruce in sand culture and in mor humus. Both increased ionic strength and increased pH may be reasons for this rather than Ca²⁺ specifically.     

Isolation of alkaliphilic calcifying bacteria and their feasibility for enhanced CaCO3 precipitation in bio-based cementitious composites

Microbially induced calcite precipitation (MICP), secreted through biological metabolic activity, secured an imperative position in remedial measures within the construction industry subsequent to ecological, environmental and economical returns. However, this contemporary recurrent healing system is susceptible to microbial depletion in the highly alkaline cementitious environment. Therefore, researchers are probing for alkali resistant calcifying microbes. In the present study, alkaliphilic microbes were isolated from different soil sources and screened for probable CaCO₃ precipitation. Non-ureolytic pathway (oxidation of organic carbon) was adopted for calcite precipitation to eliminate the production of toxic ammonia. For this purpose, calcium lactate Ca(C₃H₅O₃)₂ and calcium acetate Ca(CH₃COO)₂ were used as CaCO₃ precipitation precursors. The quantification protocol for precipitated CaCO₃ was established to select potent microbial species for implementation in the alkaline cementitious systems as more than 50% of isolates were able to precipitate CaCO₃. Results suggested 80% of potent calcifying strains isolated in this study, portrayed higher calcite precipitation at pH 10 when compared to pH 7. Ten superlative morphologically distinct isolates capable of CaCO₃ production were identified by 16SrRNA sequencing. Sequenced microbes were identified as species of Bacillus, Arthrobacter, Planococcus, Chryseomicrobium and Corynebacterium. Further, microstructure of precipitated CaCO₃ was inspected through scanning electron microscopy (SEM), X-ray diffraction (XRD) and thermal gravimetric (TG) analysis. Then, the selected microbes were investigated in the cementitious mortar to rule out any detrimental effects on mechanical properties. These strains showed maximum of 36% increase in compressive strength and 96% increase in flexural strength. Bacillus, Arthrobacter, Corynebacterium and Planococcus genera have been reported as CaCO₃ producers but isolated strains have not yet been investigated in conjunction with cementitious mortar. Moreover, species of Chryseomicrobium and Glutamicibacter were reported first time as calcifying strains.     

间伐和凋落物处理对华北落叶松人工林土壤磷形态的影响

土壤磷在维持生态系统功能稳定性中发挥重要作用,研究间伐和凋落物处理下的土壤磷组分特征及转化机理,对森林生态系统磷素管理和可持续发展具有重要意义。采用Tiessen改良的Hedley分级方法,探究了不同间伐强度(未间伐、轻度间伐、中度间伐、重度间伐)和凋落物处理(对照、加倍、去凋、切根去凋)下土壤磷形态的变化特征及其驱动因子。结果显示:随着间伐强度的增大,土壤活性磷(Resin-Pi、NaHCO_3-Pi和NaHCO_3-Po)、土壤微生物量磷和酸性磷酸酶活性呈先增加后降低的趋势,且在中度间伐最高。凋落物加倍(DL)显著增加了土壤活性磷(Resin-Pi、NaHCO_3-Pi和NaHCO_3-Po)、土壤微生物量磷和酸性磷酸酶活性。稳定态磷(HCl-Pi、浓HCl-Pi和浓HCl-Po)、残留态磷(Residual-P)不受间伐和凋落物处理的影响。冗余分析(RDA)显示,土壤微生物量磷、酸性磷酸酶活性和土壤有机碳是引起华北落叶松人工林表层土壤磷组分变化的重要因子。研究表明,适度的间伐和增加凋落物能够显著提高华北落叶松人工林表层土壤磷素的活化能力。本研究为华北落叶松人工林的可持续经营提供依据。     

Calcium carbonate precipitation and crystal morphology induced by microbial carbonic anhydrase and other biological factors

The effect of microbial carbonic anhydrase (CA) on the calcium carbonate (CaCO₃) precipitation was systematically investigated comparing to other biological factors (bovine CA, bovine serum albumin, carboxymethyl chitosan and glutamic acid). The results showed that the precipitation rate of Ca²⁺ in the presence of either microbial CA or bovine CA was faster than that in the presence of 1% bovine serum albumin, 1% carboxymethyl chitosan or 1% glutamic acid, respectively. In addition, XRD analysis indicated that the dominant CaCO₃ crystal phase was calcite. The CaCO₃ crystal morphologies mainly showed cubic and polyhedral shapes induced by microbial CA, and became multiformity induced by other factors from FE-SEM analysis. These results suggested a novel approach for biomimetic synthesis of CaCO₃ materials by microbial CA.     

Diverse communities of Bacteria and Archaea flourished in Palaeoarchaean (3.5–3.3 Ga) microbial mats

Limited taxonomic classification is possible for Archaean microbial mats and this is a fundamental limitation in constraining early ecosystems. Applying Fourier transform infrared spectroscopy (FTIR), a powerful tool for identifying vibrational motions attributable to specific functional groups, we characterized fossilized biopolymers in 3.5–3.3 Ga microbial mats from the Barberton greenstone belt (South Africa). Microbial mats from four Palaeoarchaean horizons exhibit significant differences in taxonomically informative aliphatic contents, despite high aromaticity. This reflects precursor biological heterogeneity since all horizons show equally exceptional preservation and underwent similar grades of metamorphism. Low methylene to end-methyl (CH₂/CH₃) absorbance ratios in mats from the 3.472 Ga Middle Marker horizon signify short, highly branched n-alkanes interpreted as isoprenoid chains forming archaeal membranes. Mats from the 3.45 Ga Hooggenoeg Chert H5c, 3.334 Ga Footbridge Chert, and 3.33 Ga Josefsdal Chert exhibit higher CH₂/CH₃ ratios suggesting mostly longer, unbranched fatty acids from bacterial lipid precursors. Absorbance ratios of end-methyl to methylene (CH₃/CH₂) in Hooggenoeg, Josefsdal and Footbridge mats yield a range of values (0.20–0.80) suggesting mixed bacterial and archaeal architect communities based on comparison with modern examples. Higher (0.78–1.25) CH₃/CH₂ ratios in the Middle Marker mats identify Archaea. This exceptional preservation reflects early, rapid silicification preventing the alteration of biogeochemical signals inherited from biomass. Since silicification commenced during the lifetime of the microbial mat, FTIR signals estimate the affinities of the architect community and may be used in the reconstruction of Archaean ecosystems. Together, these results show that Bacteria and Archaea flourished together in Earth's earliest ecosystems.     

Impacts of 3 years of elevated atmospheric CO2 on rhizosphere carbon flow and microbial community dynamics

Carbon (C) uptake by terrestrial ecosystems represents an important option for partially mitigating anthropogenic CO₂ emissions. Short‐term atmospheric elevated CO₂ exposure has been shown to create major shifts in C flow routes and diversity of the active soil‐borne microbial community. Long‐term increases in CO₂ have been hypothesized to have subtle effects due to the potential adaptation of soil microorganism to the increased flow of organic C. Here, we studied the effects of prolonged elevated atmospheric CO₂ exposure on microbial C flow and microbial communities in the rhizosphere. Carex arenaria (a nonmycorrhizal plant species) and Festuca rubra (a mycorrhizal plant species) were grown at defined atmospheric conditions differing in CO₂ concentration (350 and 700 ppm) for 3 years. During this period, C flow was assessed repeatedly (after 6 months, 1, 2, and 3 years) by ¹³C pulse‐chase experiments, and label was tracked through the rhizosphere bacterial, general fungal, and arbuscular mycorrhizal fungal (AMF) communities. Fatty acid biomarker analyses and RNA‐stable isotope probing (RNA‐SIP), in combination with real‐time PCR and PCR‐DGGE, were used to examine microbial community dynamics and abundance. Throughout the experiment the influence of elevated CO₂ was highly plant dependent, with the mycorrhizal plant exerting a greater influence on both bacterial and fungal communities. Biomarker data confirmed that rhizodeposited C was first processed by AMF and subsequently transferred to bacterial and fungal communities in the rhizosphere soil. Over the course of 3 years, elevated CO₂ caused a continuous increase in the ¹³C enrichment retained in AMF and an increasing delay in the transfer of C to the bacterial community. These results show that, not only do elevated atmospheric CO₂ conditions induce changes in rhizosphere C flow and dynamics but also continue to develop over multiple seasons, thereby affecting terrestrial ecosystems C utilization processes.     

Functional potential and assembly of microbes from sediments in a lake bay and adjoining river ecosystem for polycyclic aromatic hydrocarbon biodegradation

Lake and adjoining river ecosystems are ecologically and economically valuable and are heavily threatened by anthropogenic activities. Determining the inherent capacity of ecosystems for polycyclic aromatic hydrocarbon (PAH) biodegradation can help quantify environmental impacts on the functioning of ecosystems, especially on that of the microbial community. Here, PAH biodegradation potential was compared between sediments collected from a lake bay (LS) and an adjoining river (RS) ecosystem. Microbial community composition, function, and their co-occurrence patterns were also explored. In the RS, the biodegradation rates (K_D) of pyrene or PAH were almost two orders of magnitude higher than those in the LS. Sediment functional community structure and network interactions were dramatically different between the LS and RS. Although PAH degradation genes (p450aro, quinoline, and qorl) were detected in the LS, the community activity of these genes needed to be biostimulated for accelerated bioremediation. In contrast, functional communities in the RS were capable of spontaneous natural attenuation of PAH. The degradation of PAH in the RS also required coordinated response of the complex functional community. Taken together, elucidating functions and network interactions in sediment microbial communities and their responses to environmental changes are very important for the bioremediation of anthropogenic toxic contaminants.