Chlorine dioxide (ClO
2
), an alternative disinfectant to chlorine, has been widely applied in water and wastewater disinfection. This paper aims at presenting an overview of the inactivation ...kinetics and mechanisms of ClO
2
with viruses. The inactivation efficiencies vary greatly among different virus species. The inactivation rates for different serotypes within a family of viruses can differ by over 284%. Generally, to achieve a 4-log removal, the exposure doses, also being referred to as Ct values (mutiplying the concentration of ClO
2
and contact time) vary in the range of 0.06–10 mg L
−1
min. Inactivation kinetics of viruses show two phases: an initial rapid inactivation phase followed by a tailing phase. Inactivation rates of viruses increase as pH or temperature increases, but show different trends with increasing concentrations of dissolved organic matter (DOM). Both damages in viral proteins and in the 5′ noncoding region within the genome contribute to virus inactivation upon ClO
2
disinfection.
Long before bacteria infected humans, they infected amoebas, which remain a potentially important reservoir for human disease. Diverse soil amoebas including Dictyostelium and Acanthamoeba can host ...intracellular bacteria. Though the internal environment of free-living amoebas is similar in many ways to that of mammalian macrophages, they differ in a number of important ways, including temperature. A new study in PLOS Biology by Taylor-Mulneix et al. demonstrates that Bordetella bronchiseptica has two different gene suites that are activated depending on whether the bacterium finds itself in a hot mammalian or cool amoeba host environment. This study specifically shows that B. bronchiseptica not only inhabits amoebas but can persist and multiply through the social stage of an amoeba host, Dictyostelium discoideum.
Microorganisms play important roles in the biogeochemical cycling of sulphur (S), an essential element in the Earth's biosphere. Shotgun metagenome sequencing has opened a new avenue to advance our ...understanding of S cycling microbial communities. However, accurate metagenomic profiling of S cycling microbial communities remains technically challenging, mainly due to low coverage and inaccurate definition of S cycling gene families in public orthology databases. Here we developed a manually curated S cycling database (SCycDB) to profile S cycling functional genes and taxonomic groups for shotgun metagenomes. The developed SCycDB contains 207 gene families and 585,055 representative sequences affiliated with 52 phyla and 2684 genera of bacteria/archaea, and 20,761 homologous orthology groups were also included to reduce false positive sequence assignments. SCycDB was applied for functional and taxonomic analysis of S cycling microbial communities from four habitats (freshwater, hot spring, marine sediment and soil). Gene families and microorganisms involved in S reduction were abundant in the marine sediment, while those of S oxidation and dimethylsulphoniopropionate transformation were abundant in the soil. SCycDB is expected to be a useful tool for fast and accurate metagenomic analysis of S cycling microbial communities in the environment.
•This review assessed the contamination levels of PAE in various ecosystems.•Overviewed the current status of PAE-degrading bacterial isolates and communities.•Discussed the challenges for ...understanding in situ PAE biodegradation mechanisms.•Proposed a guide of building synthetic community to decipher interaction mechanism.
The extensive use of phthalic acid esters (PAEs) has led to their widespread distribution across various environments. As PAEs pose significant threats to human health, it is urgent to develop efficient strategies to eliminate them from environments. Bacteria-driven PAE biodegradation has been considered as an inexpensive yet effective strategy to restore the contaminated environments. Despite great advances in bacterial culturing and sequencing, the inherent complexity of indigenous microbial community hinders us to mechanistically understand in situ PAE biodegradation and efficiently harness the degrading power of bacteria. The synthetic microbial ecology provides us a simple and controllable model system to address this problem. In this review, we focus on the current progress of PAE biodegradation mediated by bacterial isolates and indigenous bacterial communities, and discuss the prospective of synthetic PAE-degrading bacterial communities in PAE biodegradation research. It is anticipated that the theories and approaches of synthetic microbial ecology will revolutionize the study of bacteria-driven PAE biodegradation and provide novel insights for developing effective bioremediation solutions.
A key question in cooperation is how to find the right partners and maintain cooperative relationships. This is especially challenging for horizontally transferred bacterial symbionts where ...relationships must be repeatedly established anew. In the social amoeba Dictyostelium discoideum farming symbiosis, two species of inedible Burkholderia bacteria (Burkholderia agricolaris and Burkholderia hayleyella) initiate stable associations with naive D. discoideum hosts and cause carriage of additional bacterial species. However, it is not clear how the association between D. discoideum and its carried Burkholderia is formed and maintained. Here, we look at precisely how Burkholderia finds its hosts. We found that both species of Burkholderia clones isolated from D. discoideum, but not other tested Burkholderia species, are attracted to D. discoideum supernatant, showing that the association is not simply the result of haphazard engulfment by the amoebas. The chemotactic responses are affected by both partners. We find evidence that B. hayleyella prefers D. discoideum clones that currently or previously carried Burkholderia, while B. agricolaris does not show this preference. However, we find no evidence of Burkholderia preference for their own host clone or for other hosts of their own species. We further investigate the chemical differences of D. discoideum supernatants that might explain the patterns shown above using a mass spectrometry based metabolomics approach. These results show that these bacterial symbionts are able to preferentially find and to some extent choose their unicellular partners. In addition, this study also suggests that bacteria can actively search for and target phagocytic cells, which may help us better understand how bacteria interact with immune systems.
The deep chlorophyll maximum (DCM) harbours diverse microbial communities and regulates carbon fixation and sequestration in marine ecosystems. Although variations in the DCM microbial community ...diversity and composition across oceans are reported, we still have a limited knowledge about the ecological mechanism driving the biogeography of DCM microbial communities and their contributions to ecosystem functioning.
Here, based on DNA‐sequencing data (16S rRNA and 18S rRNA genes) with two size fractions collected from coastal to offshore regions of the South China sea (SCS), we found that both size‐fractionated bacterial and protistan communities in the DCM exhibited a distance‐decay pattern, which was strongly governed by deterministic processes (62.7%–72.2%) and mainly explained by environmental factors (34.1%–37.7%).
Under warmer temperature and fresher salinity levels, the decreased abundance of protistan parasites induced the weakening parasitic interactions with other protists, whereas the increased abundance of protistan consumers enhanced the phagocytic interactions with bacteria. Such reconstruction of microbial communities induced by environmental variations was thought to constrain particulate organic carbon (POC) flux, as revealed by the partial least square regression model illustrating a strong correlation between the composition of functional protistan groups and POC content of DCM (R2 = 0.48; r = 0.75; p < 10−6).
This work highlights the importance of environmental filtering in shaping DCM microbial communities and extends our understanding of the declined carbon flux of the DCM in the SCS under future scenarios.
Read the free Plain Language Summary for this article on the Journal blog.
Read the free Plain Language Summary for this article on the Journal blog.
Soil protists are the invisible majority of soil eukaryotes, which are essential but often forgotten parts of the soil ecosystem. They play key roles in microbial food webs by predating on other soil ...microbes. However, it is not clear how dormant soil protists sense, recognize and feed on diverse microbial prey.
In this study, we used a soil amoeba, Dictyostelium discoideum, to study selective discrimination and predation of 14 different bacteria. We found that discrimination and sensing of prey in D. discoideum started as early as resting spores. Dictyostelium discoideum had higher hatching rates, formed bigger amoeba plaques and preferred high nutritional value bacteria. The feeding speed of amoeba on various bacteria was constant and was not linked with sensing of prey or bacterial nutritional value. We also found that higher bacterial density decreased predation efficiency, and one species, P. fluorescens, induced a strong density‐dependent inhibition of amoeba spore production.
In conclusion, we find that dormant D. discoideum can selectively sense and predate on different soil bacteria, a process that is likely mediated through active amoeba preference as well as bacterial inhibition. This study provides new insights into the role of protists in shaping soil bacterial communities, and future study needs to assess this in natural soil environments.
摘要
土壤原生生物是土壤真核生物的主要组成成分，其在土壤生态系统中不可或缺但又经常被忽视。它们通过捕食土壤微生物来影响土壤微食物网。但是，休眠的土壤原生生物如何感知、识别和捕食它们的猎物尚不清楚。
本研究利用一种土壤阿米巴盘基网柄菌来研究其对十四种土壤细菌的选择性识别和捕食。发现盘基网柄菌在休眠期就已经可以识别其猎物：它们对高营养的细菌有着更高的孵化率，并形成更大的捕食阿米巴斑。但盘基网柄菌的捕食速率是恒定的，与细菌识别和细菌营养价值并没有相关性。我们还发现细菌密度会影响盘基网柄菌的捕食效率。其中一种细菌，萤光假单胞菌，表现出了非常明显的随密度增高而抑制盘基网柄菌生长的情况。
总而言之，本研究发现休眠期盘基网柄菌已经可以感知和捕食不同的细菌，其背后机制是由阿米巴主动识别和细菌抑制共同决定的。本研究为原生生物如何塑造和调控土壤微生物群落提供了新的视角，未来研究需要评估自然土壤环境中二者的互作模式。
A free Plain Language Summary can be found within the Supporting Information of this article.
A free Plain Language Summary can be found within the Supporting Information of this article.
Methane is a critical greenhouse gas with significant impacts on environmental and global change. However, CH4 cycling processes and coupling mechanisms with the biogeochemical cycling of carbon, ...nitrogen, sulfur and metals in the environment remain elusive. To fill such knowledge gaps, we constructed a manually curated methane cycling database (MCycDB) for comprehensive and accurate analysis of methane cycling microbial communities. MCycDB contains 298 methane cycling gene families covering 10 methane metabolism pathways with 610,208 representative sequences, and associated reference sequences from the NCBI RefSeq database with 48 phyla and 2,197 genera, and five phyla and 100 genera for bacteria and archaea, respectively. Also, homologous groups from public orthology databases were identified and included in MCycDB to reduce false positive assignments. We applied MCycDB to profile methane cycling gene families and associated taxonomic groups from various environments. Gene families involved in methanogenesis were abundant in hot spring sediment and less abundant in freshwater, whereas the ones involved in aerobic oxidation of methane were abundant in permafrost and peatland. This study demonstrates that MCycDB is a useful tool for studying microbially‐driven methane cycling processes with high specificity, coverage and accuracy.
Clarifying mechanisms underlying the ecological succession of gut microbiota is a central theme of gut ecology. Under experimental manipulations of zebrafish hatching and rearing environments, we ...test our core hypothesis that the host development will overwhelm environmental dispersal in governing fish gut microbial community succession due to host genetics, immunology, and gut nutrient niches. We find that zebrafish developmental stage substantially explains the gut microbial community succession, whereas the environmental effects do not significantly affect the gut microbiota succession from larvae to adult fish. The gut microbiotas of zebrafish are clearly separated according to fish developmental stages, and the degree of homogeneous selection governing gut microbiota succession is increasing with host development. This study advances our mechanistic understanding of the gut microbiota assembly and succession by integrating the host and environmental effects, which also provides new insights into the gut ecology of other aquatic animals.
microRNAs (miRNAs) have been found to play an essential role in the modulation of numerous biological processes in eukaryotes. Chlamydomonas reinhardtii is an ideal model organism for the study of ...many metabolic processes including responses to sulfur-deprivation. We used a deep sequencing platform to extensively profile and identify changes in the miRNAs expression that occurred under sulfur-replete and sulfur-deprived conditions. The aim of our research was to characterize the differential expression of Chlamydomonas miRNAs under sulfur-deprived conditions, and subsequently, the target genes of miRNA involved in sulfur-deprivation were further predicted and analyzed.
By using high-throughput sequencing, we characterized the microRNA transcriptomes under sulphur-replete and sulfur-deprived conditions in Chlamydomonas reinhardtii. We predicted a total of 310 miRNAs which included 85 known miRNAs and 225 novel miRNAs. 13 miRNAs were the specific to the sulfur-deprived conditions. 47 miRNAs showed significantly differential expressions responding to sulfur-deprivation, and most were up-regulated in the small RNA libraries with sulfur-deprivation. Using a web-based integrated system (Web MicroRNAs Designer 3) and combing the former information from a transcriptome of Chlamydomonas reinhardtii, 22 miRNAs and their targets involved in metabolism regulation with sulfur-deprivation were verified.
Our results indicate that sulfur-deprivation may have a significant influence on small RNA expression patterns, and the differential expressions of miRNAs and interactions between miRNA and its targets might further reveal the molecular mechanism responding to sulfur-deprivation in Chlamydomonas reinhardtii.
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