Morphological, Microstructural, and In Situ Chemical Characteristics of Siderite Produced by Iron-Reducing Bacteria.

Dissimilatory iron-reducing bacteria (DIRB) oxidize organic matter or hydrogen and reduce ferric iron to form Fe(II)-bearing minerals, such as magnetite and siderite. However, compared with magnetite, which was extensively studied, the mineralization process and mechanisms of siderite remain unclear. Here, with the combination of advanced electron microscopy and synchrotron-based scanning transmission X-ray microscopy (STXM) approaches, we studied in detail the morphological, structural, and chemical features of biogenic siderite via a growth experiment with Shewanella oneidensis MR-4. Results showed that along with the growth of cells, Fe(II) ions were increasingly released into solution and reacted with CO32- to form micrometer-sized siderite minerals with spindle, rod, peanut, dumbbell, and sphere shapes. They are composed of many single-crystal siderite plates that are fanned out from the center of the particles. Additionally, STXM revealed Fh and organic molecules inside siderite. This suggests that the siderite crystals might assemble around a Fh-organic molecule core and then continue to grow radially. This study illustrates the biomineralization and assembly of siderite by a successive multistep growth process induced by DIRB, also provides evidences that the distinctive shapes and the presence of organic molecules inside might be morphological and chemical features for biogenic siderite.

Methanobacterium Capable of Direct Interspecies Electron Transfer.

Direct interspecies electron transfer (DIET) from bacteria to methanogens is a revolutionary concept for syntrophic metabolism in methanogenic soils/sediments and anaerobic digestion. Previous studies have indicated that the potential for DIET is limited to methanogens in the Methanosarcinales, leading to the assumption that an abundance of other types of methanogens, such as Methanobacterium species, indicates a lack of DIET. We report here on a strain of Methanobacterium, designated strain YSL, that grows via DIET in defined cocultures with Geobacter metallireducens. The cocultures formed aggregates, in which cells of strain YSL and G. metallireducens were uniformly dispersed throughout. This close association of the two species is the likely explanation for the ability of a strain of G. metallireducens that could not express electrically conductive pili to grow in coculture with strain YSL. Granular activated carbon promoted the initial formation of the DIET-based cocultures. The discovery of DIET in Methanobacterium, the genus of methanogens that has been the exemplar for interspecies electron transfer via H2, suggests that the capacity for DIET is much more broadly distributed among methanogens than previously considered. More innovative approaches to microbial isolation and characterization are needed in order to better understand how methanogenic communities function.

Inhibition effect of polyvinyl chloride on ferrihydrite reduction and electrochemical activities of Geobacter metallireducens.

Geobacter metallireducens GS15, a model of dissimilatory iron-reducing bacteria, is the key regulator in biogeochemical iron cycling. How the emerging contaminant microplastics involved in the iron cycling are driven by microbes on the microscale remains unknown. Hence, the influences of two typical microplastics, polybutylene terephthalate-hexane acid (PBAT) and polyvinyl chloride (PVC), were explored on the activity of G. metallireducens GS15 with ferrihydrite or ferric citrate as the respective electron acceptors. The results showed that the iron (II) contents in PBAT- and PVC-treatment groups were 16.79 and 6.81 mM, respectively, at the end of the experiment. Compared with the PBAT-treatment group, scanning electron microscopy and energy dispersive spectrometery revealed that merely a small amount of iron-containing products covered the surface of PVC. Moreover, PBAT and PVC could both retard the electroactivity of G. metallireducens GS15 at the beginning of microbial fuel cell operation. On the basis of the results above, microplastic PVC might exhibit potential inhibition of the iron cycling process driven by G. metallireducens GS15 with ferrihydrite as the terminal electron acceptor. This study extended our understanding of the influence of the microplastics PBAT and PVC on microbially mediated biogeochemical iron cycling. The findings might have an important implication on the biogeochemical elements cycling in the ecosystem with the involvement of emerging contaminant microplastics.

[Semen quality and HIV RNA level in HIV/AIDS male patients after treated by highly active antiretroviral therapy].

OBJECTIVE: To evaluate the semen quality of the HIV/AIDS male patients after treated by the highly active antiretroviral therapy (HAART) and their potential of transmitting HIV/AIDS and provide some evidence for this cohort of males who wish for parenthood. METHODS: We collected semen samples from 20 HIV/AIDS male patients who had been treated by HAART for over 6 months and wished for parenthood. We examined sperm concentration, viability and total motility and the percentage of morphologically normal sperm (MNS) using the computer-assisted semen analysis system, measured the HIV-1 RNA loads in the semen by the Cobas Amplicor Monitor test, and counted CD4+ T cells in the peripheral blood by flow cytometry. RESULTS: The patients were aged 25－40 (30.7 ± 5.05) years. After treated by HAART for 6－26 (14.24 ± 12.26) months, the count of blood CD4+ T cells was significantly increased (341－1 058 ï¼»535.76 ± 212.021ï¼½ /µl) in comparison with the baseline (226－965 ï¼»422.38 ± 200.86ï¼½ /µl). Compared with the normal value, the semen volume was increased except in 1 case (≥2 ml) while total sperm motility was decreased in 13 cases (≥40%), and so were sperm concentration in 2 cases (≥15 × 106 / ml), sperm viability in 5 (58%), the percentage of progressively motile sperm in 18 (≥32%), and the percentage of MNS in 6 (≤4%). HIV-1 RNA in the peripheral blood was <20 copies/mL in all the cases and that in the seminal plasma was also <20 copies/ml in 18 cases but >20 copies/mL in the other 2 (ï¼»4.70 × 101ï¼½ and ï¼»2.2 × 102ï¼½ copies/ml, respectively). Of the 4 couples that had sex without protective measures for over 6 months, all the 4 female partners exhibited negative HIV antibodies in regular follow-up examinations and 1 achieved spontaneous pregnancy and healthy birth, with negative HIV-1 RNA in both the mother and the baby. CONCLUSIONS: The HIV RNA level is higher in the semen than in the blood of the HIV/AIDS male patients after HAART, which indicates the potential risk of their semen transmitting HIV/AIDS to their female partners. Their sperm concentration and total sperm motility are lower than the normal value, which suggests a decreased fertility.

Spatial variation in bacterial community in natural wetland-river-sea ecosystems.

Wetland-estuarine-marine environments are typical oxic/anoxic transition zones and have complex water flow-paths within the zone of mixing where freshwater interacts with ocean water. Little is known about the impact of this interaction on bacterial community structures or the relationship between bacterial community and geochemical factors in such transitional mixing environments. Hence, we investigated the distribution patterns and diversity in bacterial communities in the Yellow River estuary-coastal wetland-Bohai Sea transition zone by analyzing 39 samples from 13 ordered sites. High-throughput sequencing of the 16S rRNA gene revealed significant shifts in diversity and distribution of bacterial community in sediments from the Yellow River estuary to the Bohai Sea. Yellow River sediment was dominated by hydrogen-, nitrogen-, and iron-cycling bacteria, such as Hydrogenophaga, Nitrospira, Pseudomonas, and Thiobacillus. The coastal wetland had a haloduric community associated with different functions, such as Planctomyces, Marinobacter, Halomonas, Salinivibrio, and Salinibacter. The Bohai Sea sediment had a higher relative abundance of Lutimonas, Desulfococcus, Photobacterium, Propionigenium, and Vibrio. Spatial variation in bacterial community was correlated with pH, salinity and sulfate (SO42-) concentration in such coastal environments. The major bacterial taxa were significantly different across the wetland, estuary, and coastal marine ecosystems, indicating substantial spatial heterogeneity among the three ecosystems. Statistical analysis revealed strong links between variation in bacterial community structure and ecosystem type. Our results demonstrate the importance of geographic and geochemical factors in structuring the bacterial community in natural environments.

Electrochemically active iron (III)-reducing bacteria in coastal riverine sediments.

Iron (III)-reducing bacteria (IRB) play significant roles in the degradation of naturally occurring organic matter and in the cycling of heavy metals in marine and freshwater sediments. Our previous study has demonstrated the co-occurrence of Geobacteraceae and Methanosarcinamazei as aggregates in the iron (III)-reducing enrichments from a coastal gold mining site on the Jiehe River. The IRB community in the enriched sediments was dominated by members of Comamonadacea, Clostridiaceae, Bacillaceae, Bacteroidaceae, and Geobacteraceae. Furthermore, four representative strains (JhA, JhB, JhC-1, and JhC-2) were isolated and found to belong to the genus of Anaerosinus, Bacillus, and Clostridium with 97.31-98.82% identity of 16S rRNA genes. The iron (III)-reducing ability of all these isolates was identified. Interestingly, JhA showed electrochemical activity with chronoamperometry (CA) and cyclic voltammetry (CV), indicating its ability to oxidize ethanol, liberate, and transfer electrons, thus, expanding our knowledge of a new genus with electrochemical activity. The results revealed the cultivability and electrochemical activity of IRB in coastal riverine sediment and indicated that JhA was an unknown extracellular electron producer with the ability to reduce iron (III). This study expands our knowledge of the electrochemical characterization of the genus Anaerosinus. It is reasonable to expect that these isolates have potential applications in heavy metal bioremediation operations in natural environments.

Analysis of small RNAs derived from Chinese wheat mosaic virus.

The virus-derived small interfering RNAs (vsiRNAs) of Chinese wheat mosaic virus (CWMV), a member of the genus Furovirus, were characterised from wheat plants by deep sequencing. CWMV vsiRNAs of 21-22 nt in length predominated, suggesting that there might be a conserved mechanism of DCL2 and DCL4 involvement in the biogenesis of vsiRNAs, as well as a common RNA silencing pathway in CWMV-infected wheat plants. The 5'-terminal base of vsiRNAs was biased towards A/U, suggesting that CWMV vsiRNAs might be loaded into diverse AGO-containing RISCs to disturb the gene expression of host plants. Possible targets for some of the vsiRNAs were predicted.

UBE2J1 promotes ALV-A proviral DNA synthesis through the STAT3/IRF1 signaling pathway.

The ubiquitin-binding enzyme E2J1 is located on the endoplasmic reticulum membrane. It plays a role in transport throughout the process of ubiquitination. In mammals, UBE2J1 can promote RNA virus replication. However, the biological function of chicken UBE2J1 is unclear. In this study, chicken UBE2J1 was cloned for the first time, and UBE2J1 overexpression and shRNA knockdown plasmids were constructed. In chicken embryo fibroblasts, overexpression of UBE2J1 promoted the replication of subtype A avian leukosis virus, while knockdown of UBE2J1 inhibited the replication of ALV-A virus. In addition, we divided virus replication into virus adsorption and invasion into DF-1 cells, synthesis of proviral DNA, and release of viral particles. UBE2J1 promoted the replication of ALV-A virus by promoting the synthesis of proviral DNA. This result was caused by UBE2J1 inhibiting the production of interferon by inhibiting the STAT3/IRF1 pathway. We mutated ser at position 184 of UBE2J1 to Gly and found that this site plays a role as the phosphorylation site of UBE2J1. We confirmed that UBE2J1 promotes ALV-A replication in chicken embryo fibroblasts by inhibiting the STAT3/IRF1 pathway. This study provides new ideas and insights into ubiquitin-related proteins and antiviral immunity.

Effectively facilitating the degradation of chloramphenicol by the synergism of Shewanella oneidensis MR-1 and the metal-organic framework.

Electroactive bacteria (EAB) and metal oxides are capable of synergistically removing chloramphenicol (CAP). However, the effects of redox-active metal-organic frameworks (MOFs) on CAP degradation with EAB are not yet known. This study investigated the synergism of iron-based MOFs (Fe-MIL-101) and Shewanella oneidensis MR-1 on CAP degradation. 0.5 g/L Fe-MIL-101 with more possible active sites led to a three-fold higher CAP removal rate in the synergistic system with MR-1 (initial bacterial concentration of 0.2 at OD600), and showed a superior catalytic effect than exogenously added Fe(III)/Fe(II) or magnetite. Mass spectrometry revealed that CAP was transformed into smaller molecular weight and less toxic metabolites in cultures. Transcriptomic analysis showed that Fe-MIL-101 enhanced the expression of genes related to nitro and chlorinated contaminants degradation. Additionally, genes encoding hydrogenases and c-type cytochromes associated with extracellular electron transfer were significantly upregulated, which may contribute to the simultaneous bioreduction of CAP both intracellularly and extracellularly. These results indicated that Fe-MIL-101 can be used as a catalyst to synergize with EAB to effectively facilitate CAP degradation, which might shed new light on the application in the in situ bioremediation of antibiotic-contaminated environments.

Transport of intensity phase imaging from multiple noisy intensities measured in unequally-spaced planes.

The noise problem is generally inevitable for phase retrieval by solving the transport of intensity equation (TIE). The noise effect can be alleviated by using multiple intensities to estimate the axial intensity derivative in the TIE. In this study, a method is proposed for estimating the intensity derivative by using multiple unevenly-spaced noisy measurements. The noise-minimized intensity derivative is approximated by a linear combination of the intensity data, in which the coefficients are obtained by solving a constrained optimization problem. The performance of the method is investigated by both the error analysis and the numerical simulations, and the results show that the method can reduce the noise effect on the retrieved phase. In addition, guidelines for the choice of the number of the intensity planes are given.

Atmospheric spectral model and theoretical expressions of irradiance scintillation index for optical wave propagating through moderate-to-strong non-Kolmogorov turbulence.

A new atmospheric spectral model and expressions of irradiance scintillation index are derived theoretically for optical wave propagating through moderate-to-strong non-Kolmogorov turbulence. They are developed under Andrews' assumption that small-scale irradiance fluctuations are modulated by large-scale irradiance fluctuations of the wave, and the geometrical optics approximation is adopted for mathematical development. A wide range of turbulence strength is considered instead of a limited range for weak turbulence. The atmospheric spectral model has a spectral power law value in the range of 3 to 4 instead of the standard power law value of 11/3. Numerical calculations are conducted to analyze the influences of spectral power law and turbulence strength.

Transport of intensity phase imaging from multiple intensities measured in unequally-spaced planes.

A method based on the transport of intensity equation (TIE) for phase retrieval is presented, which can retrieve the optical phase from intensity measurements in multiple unequally-spaced planes in the near-field region. In this method, the intensity derivative in the TIE is represented by a linear combination of intensity measurements, and the coefficient of the combination can be expressed by explicitly analytical form related to the defocused distances. The proposed formula is a generalization of the TIE with high order intensity derivatives. The numerical experiments demonstrate that the proposed method can improve the accuracy of phase retrieval with higher-order intensity derivatives and is more convenient for practical application.

Irradiance scintillation for Gaussian-beam wave propagating through weak non-Kolmogorov turbulence.

Kolmogorov turbulence theory based models cannot be directly applied in non-Kolmogorov turbulence case, which has been reported recently by increasing experimental evidence and theoretical investigation. In this study, based on the generalized von Karman spectral model, the theoretical expression of the irradiance scintillation index is derived for Gaussian-beam wave propagating through weak non-Kolmogorov turbulence with horizontal path. In the derivation, the expression is divided into two parts for physical analysis purpose and mathematical analysis convenience. This expression considers the influences of finite turbulence inner and outer scales and has a general spectral power law value in the range 3 to 4 instead of standard power law value of 11/3 (for Kolmogorov turbulence). Numerical simulations are conducted to investigate the influences.

Complete Genome Sequence of Methanobacterium electrotrophus Strain YSL, Isolated from Coastal Riverine Sediments.

Methanobacterium electrotrophus strain YSL was isolated from enriched microbial aggregates from a coastal riverine sediment sample from Shandong Province, China. The genome of YSL was sequenced with the PacBio Sequel platform and contained three plasmids in addition to the chromosome. A total of 2,521 protein-coding genes and 58 RNA genes were predicted.

Desulfovibrio feeding Methanobacterium with electrons in conductive methanogenic aggregates from coastal zones.

Geobacter, as a typical electroactive microorganism, is the "engine" of interspecies electron transfer (IET) between microorganisms. However, it does not have a dominant position in all natural environments. It is not known what performs a similar function as Geobacter in coastal zones. Metagenomic and metatranscriptomic analysis revealed that Desulfovibrio and Methanobacterium species were the most abundant in electrochemically active aggregates. Metatranscriptomic analysis showed that Desulfovibrio species highly expressed genes for ethanol metabolism and extracellular electron transfer involving cytochromes, pili and flagella. Methanobacterium species in the aggregates also expressed genes for enzymes involved in reducing carbon dioxide to methane. Pure cultures demonstrated that the isolated Desulfovibrio sp. strain JY contributed to aggregate conductivity and directly transferred electrons to Methanothrix harundinacea, which is unable to use H2 or formate. Most importantly, further coculture studies indicated that Methanobacterium strain YSL might directly accept electrons from the Desulfovibrio strain JY for the reduction of carbon dioxide to methane in the aggregate. This finding suggested that the possibility of DIET by Desulfovibrio similar to Geobacter species in conductive methanogenic aggregates can not be excluded.

Comparative genomic analysis reveals metabolic flexibility of Woesearchaeota.

The archaeal phylum Woesearchaeota, within the DPANN superphylum, includes phylogenetically diverse microorganisms that inhabit various environments. Their biology is poorly understood due to the lack of cultured isolates. Here, we analyze datasets of Woesearchaeota 16S rRNA gene sequences and metagenome-assembled genomes to infer global distribution patterns, ecological preferences and metabolic capabilities. Phylogenomic analyses indicate that the phylum can be classified into ten subgroups, termed A-J. While a symbiotic lifestyle is predicted for most, some members of subgroup J might be host-independent. The genomes of several Woesearchaeota, including subgroup J, encode putative [FeFe] hydrogenases (known to be important for fermentation in other organisms), suggesting that these archaea might be anaerobic fermentative heterotrophs.

Effects of Organic Phosphorus on Methylotrophic Methanogenesis in Coastal Lagoon Sediments With Seagrass (Zostera marina) Colonization.

Methanogens are the major contributors of greenhouse gas methane and play significant roles in the degradation and transformation of organic matter. These organisms are particularly abundant in Swan Lake, which is a shallow lagoon located in Rongcheng Bay, Yellow Sea, northern China, where eutrophication from overfertilization commonly results in anoxic environments. High organic phosphorus content is a key component of the total phosphorus in Swan Lake and is possibly a key factor affecting the eutrophication and carbon and nitrogen cycling in Swan Lake. The effects of organic phosphorus on eutrophication have been well-studied with respect to bacteria, such as cyanobacteria, unlike the effects of organic phosphorus on methanogenesis. In this study, different sediment layer samples of seagrass-vegetated and unvegetated areas in Swan Lake were investigated to understand the effects of organic phosphorus on methylotrophic methanogenesis. The results showed that phytate phosphorus significantly promoted methane production in the deepest sediment layer of vegetated regions but suppressed it in unvegetated regions. Amplicon sequencing revealed that methylotrophic Methanococcoides actively dominated in all enrichment samples from both regions with additions of trimethylamine or phytate phosphorus, whereas methylotrophic Methanolobus and Methanosarcina predominated in the enrichments obtained from vegetated and unvegetated sediments, respectively. These results prompted further study of the effects of phytate phosphorus on two methanogen isolates, Methanolobus psychrophilus, a type strain, Methanosarcina mazei, an isolate from Swan Lake sediments. Cultivation experiments showed that phytate phosphorus could inhibit methane production by M. psychrophilus but promote methane production by M. mazei. These culture-based studies revealed the effects of organic phosphorus on methylotrophic methanogenesis in coastal lagoon sediments and improves our understanding of the mechanisms of organic carbon cycling leading to methanogenesis mediated by organic phosphorus dynamics in coastal wetlands.

Multi-walled carbon nanotubes accelerate interspecies electron transfer between Geobacter cocultures.

Carbon nanotubes (CNTs) have been reported to promote symbiotic metabolism in bacteria by accelerating interspecies electron transfer. However, this phenomenon has not been investigated or proven in a cocultures system. In this study, multi-walled CNTs (MWCNTs) were added into Geobacter cocultures systems with the ability of direct interspecies electron transfer (DIET). Results showed that addition of MWCNTs accelerated the metabolic rate of the cocultures. Succinate production rate in a test with 1.0gL-1 MWCNTs was 1.12mM d-1, 1.67 times higher than without MWCNTs. However, the biotoxicity effect became evident with the addition of much higher levels of MWCNTs addition. This study supports the possibility that carbon nanotubes accelerate interspecies electron transfer and provides a theoretical basis for the MWCNTs application in the process of anaerobic wastewater treatment.

Anaerobic Bacterial Immobilization and Removal of Toxic Sb(III) Coupled With Fe(II)/Sb(III) Oxidation and Denitrification.

Antimony (Sb) pollution is a worldwide problem. In some anoxic sites, such as Sb mine drainage and groundwater sediment, the Sb concentration is extremely elevated. Therefore, effective Sb remediation strategies are urgently needed. In contrast to microbial aerobic antimonite [Sb(III)] oxidation, the mechanism of microbial anaerobic Sb(III) oxidation and the effects of nitrate and Fe(II) on the fate of Sb remain unknown. In this study, we discovered the mechanism of anaerobic Sb(III) oxidation coupled with Fe(II) oxidation and denitrification in the facultative anaerobic Sb(III) oxidizer Sinorhizobium sp. GW3. We observed the following: (1) under anoxic conditions with nitrate as the electron acceptor, strain GW3 was able to oxidize both Fe(II) and Sb(III) during cultivation; (2) in the presence of Fe(II), nitrate and Sb(III), the anaerobic Sb(III) oxidation rate was remarkably enhanced, and Fe(III)-containing minerals were produced during Fe(II) and Sb(III) oxidation; (3) qRT-PCR, gene knock-out and complementation analyses indicated that the arsenite oxidase gene product AioA plays an important role in anaerobic Sb(III) oxidation, in contrast to aerobic Sb(III) oxidation; and (4) energy-dispersive X-ray spectroscopy (EDS), X-ray photoelectron spectroscopy (XPS) and powder X-ray diffraction (XRD) analyses revealed that the microbially produced Fe(III) minerals were an effective chemical oxidant responsible for abiotic anaerobic Sb(III) oxidation, and the generated Sb(V) was adsorbed or coprecipitated on the Fe(III) minerals. This process included biotic and abiotic factors, which efficiently immobilize and remove soluble Sb(III) under anoxic conditions. The findings revealed a significantly novel development for understanding the biogeochemical Sb cycle. Microbial Sb(III) and Fe(II) oxidation coupled with denitrification has great potential for bioremediation in anoxic Sb-contaminated environments.

Trophic strategy of diverse methanogens across a river-to-sea gradient.

Methanogens are an important biogenic source of methane, especially in estuarine waters across a river-to-sea gradient. However, the diversity and trophic strategy of methanogens in this gradient are not clear. In this study, the diversity and trophic strategy of methanogens in sediments across the Yellow River (YR) to the Bohai Sea (BS) gradient were investigated by high-throughput sequencing based on the 16S rRNA gene. The results showed that the diversity of methanogens in sediments varied from multitrophic communities in YR samples to specific methylotrophic communities in BS samples. The methanogenic community in YR samples was dominated by Methanosarcina, while that of BS samples was dominated by methylotrophic Methanococcoides. The distinct methanogens suggested that the methanogenic community of BS sediments did not originate from YR sediment input. High-throughput sequencing of the mcrA gene revealed that active Methanococcoides dominated in the BS enrichment cultures with trimethylamine as the substrate, and methylotrophic Methanolobus dominated in the YR enrichment cultures, as detected to a limited amount in in situ sediment samples. Methanosarcina were also detected in this gradient sample. Furthermore, the same species of Methanosarcina mazei, which was widely distributed, was isolated from the area across a river-to-sea gradient by the culture-dependent method. In summary, our results showed that a distribution of diverse methanogens across a river-to-sea gradient may shed light on adaption strategies and survival mechanisms in methanogens.