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Life, its origin, and its distribution: a perspective from the Conway-Kochen Theorem and the Free Energy Principle.
Q2 Agricultural and Biological Sciences Pub Date : 2025-02-17 eCollection Date: 2025-01-01 DOI: 10.1080/19420889.2025.2466017
Chris Fields, Michael Levin

We argue here that the Origin of Life (OOL) problem is not just a chemistry problem but is also, and primarily, a cognitive science problem. When interpreted through the lens of the Conway-Kochen theorem and the Free Energy Principle, contemporary physics characterizes all complex dynamical systems that persist through time as Bayesian agents. If all persistent systems are to some - perhaps only minimal - extent cognitive, are all persistent systems to some extent alive, or are living systems only a subset of cognitive systems? We argue that no bright line can be drawn, and we re-assess, from this perspective, the Fermi paradox and the Drake equation. We conclude that improving our abilities to recognize and communicate with diverse intelligences in diverse embodiments, whether based on familiar biochemistry or not, will either resolve or obviate the OOL problem.

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引用次数: 0
The need for a new perspective on decision-making in bacteria.
Q2 Agricultural and Biological Sciences Pub Date : 2025-02-12 eCollection Date: 2025-01-01 DOI: 10.1080/19420889.2025.2463926
Sibin Mathew Nesin, Mathew Chandrankunnel

The individualistic and collectivistic intelligent behaviors observed in mammals, birds, and fishes have been appreciated by many scientists in recent years and supported by the Cambridge Declaration on Consciousness in 2012. Behavioral studies in lower organisms like arthropods and cephalopods showed the presence of multisensory integration, decision-making, and goal-directed behavior in these non-vertebrate animals. The presence of intelligent and history-dependent behaviors has been studied in microorganisms, and recent studies propose the possibility of cognition in single cellular organisms. The Cellular Basis of Consciousness (CBC), proposed by Arthur Reber in 2016 and elaborated by Baluška and Reber in 2019, suggests the possibility of consciousness in single cellular organisms. However, the critics of the Cellular Basis of Consciousness theory state that the individual bacterial cell does not make choices, and the decision-making is the result of stochastic differences in protein levels. Here, we want to address the criticism of decision-making in bacteria. An attempt is made to give a new perspective to the existing model to explain the flexibility in bacterial behavior in an ever-changing environment. The authors would like to consider an alternative perspective on flexibility in decision-making as the result of multiple pathways that have convergence and divergence as observed in the brain. Flexibility provides the possibility to have individualistic behavior, and the existence of such pathways can be considered as the molecular mechanism underlying individualistic decision-making in bacteria as well as in humans.

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引用次数: 0
Structure simulation-based comparison of active site variations in fungal ornithine decarboxylases.
Q2 Agricultural and Biological Sciences Pub Date : 2025-01-31 eCollection Date: 2025-01-01 DOI: 10.1080/19420889.2025.2458872
Min Jeong Kim, Jeong Ho Chang

Polyamines play crucial roles in various biological processes, including cell proliferation and differentiation, immune response modulation, and signal transduction. Ornithine decarboxylase (ODC) initiates polyamine biosynthesis by catalyzing the conversion of ornithine to putrescine in a pyridoxal phosphate (PLP)-dependent manner. While the structures of mammalian and protozoan ODCs have been elucidated, fungal ODCs remain uncharacterized. In this study, AlphaFold2 was employed to simulate the structures of ODCs from four fungi: Kluyveromyces lactis, Candida albicans, Debaryomyces hansenii, and Schizosaccharomyces pombe. The results indicated that, although these ODCs share α/β-barrel and β-sheet domains, their active site conformations exhibit subtle differences. Additionally, substrate selectivity among ODCs and related decarboxylases varied depending on the distance between the Cα of aspartate or glutamate residues within the specificity helix and the C4α of PLP. Notably, the bacterial Campylobacter jejuni decarboxylase (CjCANSDC), which binds the largest substrate, exhibits the longest distance, whereas fungal ODC, which binds the smallest substrate, displays the shortest distance. Furthermore, significant differences in the composition of amino acid residues within the active sites were also observed. This study provides insights into the structural diversity and catalytic activity of ODCs across a broad range of organisms, advancing the understanding of structure-dependent evolutionary processes.

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引用次数: 0
Extract from endophytic Fusarium isolates stimulates seed germination of the host and protocorm development of non-host orchids. 内生真菌镰刀菌提取物促进寄主种子萌发和非寄主兰花原球茎发育。
Q2 Agricultural and Biological Sciences Pub Date : 2024-12-17 eCollection Date: 2025-01-01 DOI: 10.1080/19420889.2024.2439798
Sujit Shah, Mukti Ram Paudel, Bir Bahadur Thapa, Harshita Sharma, Arun Kumar Kashyap, Bhagwan Narayan Rekadwad, Rohit Sharma, Jyotsna Sharma, Bijaya Pant

We isolated endophytic Fusarium strains from the healthy roots, stems, and leaves of Dendrobium moschatum to investigate their plant growth-promoting activities in vitro. Subsequently, Indole acetic acid (IAA) was quantified and the IaaM gene (responsible for IAA synthesis in fungi) was amplified and sequenced. Finally, a germination assay was performed with seeds of D. moschatum and a plant growth assay with protocorms of Dendrobium longicornu to test their plant growth-promoting activities. Five Fusarium isolates (CDS11, PDL1, PDL3, PDR6, PDR7) were identified in this study. The highest amount (60µgml-1) of indole acetic acid was recorded in the PDR7 extract, whereas it was not detected in PDR6 and CDS11. The fungal extracts of isolates PDR6 and PDR7 were highly effective for seed germination by approximately 80% and 90% (respectively) of the host plant. The fungal extract of PDR7 showed a high IAA content and promoted in vitro seed germination of the host (D. moschatum) and protocorm development of the non-host (D. longicornu). In contrast, IAA content in the fungal extract of PDR6 remained undetected but was effective in both seed germination and protocorm development. Our results demonstrated the potential beneficial application of endophytic Fusarium in orchid mass propagation.

从石斛的健康根、茎和叶中分离内生镰刀菌菌株,研究其体外促生活性。随后,我们对吲哚乙酸(IAA)进行了定量分析,并对真菌中负责IAA合成的iam基因进行了扩增和测序。最后,对石斛种子进行萌发试验,对石斛原球茎进行植物生长试验,考察其促进植物生长的活性。本研究共分离到5株镰刀菌(CDS11、PDL1、PDL3、PDR6、PDR7)。PDR7提取物中吲哚乙酸含量最高(60µgml-1),而PDR6和CDS11提取物中未检测到吲哚乙酸。分离菌株PDR6和PDR7的真菌提取物对寄主植物的种子萌发率分别约为80%和90%。PDR7真菌提取物具有较高的IAA含量,能促进寄主(D. moschatum)的离体种子萌发和非寄主(D. longicornu)的原球茎发育。相比之下,PDR6真菌提取物中IAA含量未检测到,但对种子萌发和原球茎发育均有影响。结果表明,内生镰刀菌在兰花群体繁殖中具有潜在的有益应用前景。
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引用次数: 0
Quorum sensing and antibiotic resistance in polymicrobial infections. 多微生物感染中的法定人数感应和抗生素耐药性。
Q2 Agricultural and Biological Sciences Pub Date : 2024-10-17 eCollection Date: 2024-01-01 DOI: 10.1080/19420889.2024.2415598
Sunny Cui, Esther Kim

Quorum sensing (QS) is a critical bacterial communication system regulating behaviors like biofilm formation, virulence, and antibiotic resistance. This review highlights QS's role in polymicrobial infections, where bacterial species interactions enhance antibiotic resistance. We examine QS mechanisms, such as acyl-homoserine lactones (AHLs) in Gram-negative bacteria and autoinducing peptides (AIPs) in Gram-positive bacteria, and their impact on biofilm-associated antibiotic resistance. The challenges uniquely associated with polymicrobial infections, such as those found in cystic fibrosis lung infections, chronic wound infections, and medical device infections, are also summarized. Furthermore, we explore various laboratory models, including flow cells and dual-species culture models, used to study QS interactions in polymicrobial environments. The review also discusses promising quorum sensing inhibitors (QSIs), such as furanones and AHL analogs, which have demonstrated efficacy in reducing biofilm formation and virulence in laboratory and clinical studies. By addressing the interplay between QS and antibiotic resistance, this paper aims to advance therapeutic strategies that disrupt bacterial communication and improve antibiotic efficacy, ultimately mitigating the global challenge of antibiotic resistance in polymicrobial infections.

法定量感应(QS)是一种重要的细菌通讯系统,可调节生物膜的形成、毒力和抗生素耐药性等行为。本综述强调了 QS 在多微生物感染中的作用,在多微生物感染中,细菌物种间的相互作用会增强抗生素耐药性。我们研究了 QS 机制,如革兰氏阴性细菌中的酰基高丝氨酸内酯(AHLs)和革兰氏阳性细菌中的自诱导肽(AIPs),以及它们对生物膜相关抗生素耐药性的影响。我们还总结了与多微生物感染有关的独特挑战,如囊性纤维化肺部感染、慢性伤口感染和医疗器械感染。此外,我们还探讨了用于研究多微生物环境中 QS 相互作用的各种实验室模型,包括流动细胞和双物种培养模型。本综述还讨论了呋喃酮类和 AHL 类似物等前景看好的法定量感应抑制剂 (QSI),这些抑制剂在实验室和临床研究中已显示出减少生物膜形成和毒力的功效。通过探讨 QS 与抗生素耐药性之间的相互作用,本文旨在推进治疗策略,破坏细菌交流并提高抗生素疗效,最终缓解多微生物感染中抗生素耐药性带来的全球性挑战。
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引用次数: 0
Synergistic effect of nano-potassium and chitosan as stimulants inducing growth and yield of bird of paradise (Sterlitiza reginae L.) in newly lands. 纳米钾和壳聚糖作为促进剂对新土地上天堂鸟(Sterlitiza reginae L.)的生长和产量的协同效应。
Q2 Agricultural and Biological Sciences Pub Date : 2024-09-26 eCollection Date: 2024-01-01 DOI: 10.1080/19420889.2024.2406754
Eman A Swedan, Kholoud Shible, Yassin M Yassin, Aleksandra Glowacka, Mohamed A A Ahmed

The bird of paradise plant is a clumping tropical species native to South Africa. It is a dramatic plant with distinctive iridescent orange and midnight blue flowers that resemble an exotic bird peeking out from the broad leaves in autumn, winter and spring. An experiment was conducted during the two seasons of 2021 and 2022 at a private farm in Damanhour, Beheira Governorate, Egypt (31"°" 04 "°"N, 30"°" 47' °E) to study the effect different concentrations of nano-potassium and chitosan and their combinations on the bird of Paradise (Sterlitiza reginae). The experiment was conducted in a randomized complete block in a split-plot design with five replicates; nano-potassium was used at 0, 100, 150, and 200 mg/l and assigned to the main plots, whereas the sub-plots involved 0, 0.25, 0.50 and 0.75 g/l of chitosan. An increase in plant height and leaf length was recorded when the plants were treated with 200 mg/l nano-potassium and 0.75 g/l chitosan. Spraying plants with concentrations of 150 mg/l nano-potassium and 0.75 g/l chitosan is associated with the superiority of S. reginae plants in other traits, such as leaves wide, number of leaves/plant, days to flowering, number of inflorescence/plant, number of florets/inflorescence, stalk length and diameter, inflorescence weight, longevity of inflorescence, and flowering period, compared to the other treatments. We conclude that adding nano-potassium and/or chitosan to the bird of paradise plant leads to an improvement in terms of vegetative and yield characteristics under newly reclaimed lands.

天堂鸟是一种丛生的热带植物,原产于南非。它是一种引人注目的植物,在秋季、冬季和春季开出独特的彩虹色橙色和午夜蓝色花朵,就像一只异国鸟儿从宽大的叶子中探出头来。2021 年和 2022 年两季,在埃及贝希拉省(31"°" 04"°"N,30"°" 47'°E)达曼胡尔的一个私人农场进行了一项实验,研究不同浓度的纳米钾和壳聚糖及其组合对天堂鸟(Sterlitiza reginae)的影响。实验采用随机完全区组,分小区设计,五次重复;纳米钾的浓度分别为 0、100、150 和 200 毫克/升,并分配到主小区,而副小区的壳聚糖浓度分别为 0、0.25、0.50 和 0.75 克/升。用 200 毫克/升纳米钾和 0.75 克/升壳聚糖处理植物时,植株高度和叶长都有所增加。与其他处理相比,喷洒浓度为 150 毫克/升纳米钾和 0.75 克/升壳聚糖的 S. reginae 植物在叶宽、叶片数/植株、开花天数、花序数/植株、小花数/花序、花柄长度和直径、花序重量、花序寿命和花期等其他性状方面更胜一筹。我们的结论是,在新开垦的土地上向天堂鸟植物添加纳米钾和/或壳聚糖可改善其植株和产量特性。
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引用次数: 0
Hypersensitivity to man-made electromagnetic fields (EHS) correlates with immune responsivity to oxidative stress: a case report. 对人造电磁场(EHS)的超敏反应与氧化应激的免疫反应相关:一份病例报告。
Q2 Agricultural and Biological Sciences Pub Date : 2024-08-04 eCollection Date: 2024-01-01 DOI: 10.1080/19420889.2024.2384874
Thawatchai Thoradit, Marthe Chabi, Blanche Aguida, Soria Baouz, Verene Stierle, Marootpong Pooam, Stephane Tousaints, Casimir D Akpovi, Margaret Ahmad

There is increasing evidence that exposure to weak electromagnetic fields (EMFs) generated by modern telecommunications or household appliances has physiological consequences, including reports of electromagnetic field hypersensitivity (EHS) leading to adverse health effects. Although symptoms can be serious, no underlying mechanism for EHS is known and there is no general cure or effective therapy. Here, we present the case study of a self-reported EHS patient whose symptoms include severe headaches, generalized fatigue, cardiac arrhythmia, attention and memory deficit, and generalized systemic pain within minutes of exposure to telecommunications (Wifi, cellular phones), high tension lines and electronic devices. Tests for cerebral, cardiovascular, and other physiological anomalies proved negative, as did serological tests for inflammation, allergies, infections, auto-immune conditions, and hormonal imbalance. However, further investigation revealed deficits in cellular anti-oxidants and increased radical scavenging enzymes, indicative of systemic oxidative stress. Significantly, there was a large increase in circulating antibodies for oxidized Low-Density Lipoprotein (LDLox), byproducts of oxidative stress accumulating in membranes of vascular cells. Because a known primary effect of EMF exposure is to increase the concentration of cellular oxidants, we propose that pathology in this patient may be causally related to a resulting increase in LDLox synthesis. This in turn could trigger an exaggerated auto-immune response consistent with EHS symptoms. This case report thereby provides a testable mechanistic framework for EHS pathology with therapeutic implications for this debilitating and poorly understood condition.

越来越多的证据表明,暴露于现代电信或家用电器产生的微弱电磁场(EMF)会产生生理后果,包括有关电磁场过敏症(EHS)导致不良健康影响的报道。虽然症状可能很严重,但 EHS 的潜在机制尚不清楚,也没有普遍的治疗方法或有效疗法。在这里,我们将介绍一位自我报告的 EHS 患者的病例研究,该患者的症状包括严重头痛、全身乏力、心律失常、注意力和记忆力减退,以及在暴露于电信(Wifi、手机)、高压线和电子设备后几分钟内出现全身疼痛。对大脑、心血管和其他生理异常的检测结果呈阴性,对炎症、过敏、感染、自身免疫疾病和内分泌失调的血清检测结果也呈阴性。然而,进一步的调查显示,细胞抗氧化剂不足,自由基清除酶增加,表明存在全身性氧化应激。值得注意的是,氧化低密度脂蛋白(LDLox)的循环抗体大量增加,而LDLox是氧化压力在血管细胞膜中累积的副产品。由于已知暴露于电磁场的主要影响是增加细胞氧化剂的浓度,我们认为该患者的病理变化可能与由此导致的低密度脂蛋白合成增加有因果关系。这反过来又会引发与 EHS 症状一致的夸张的自身免疫反应。因此,本病例报告为 EHS 病理学提供了一个可检验的机理框架,并对这种使人衰弱且鲜为人知的病症具有治疗意义。
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引用次数: 0
Emergence of information processing in biological systems and the origin of life. 生物系统中信息处理的出现和生命的起源。
Q2 Agricultural and Biological Sciences Pub Date : 2024-07-10 eCollection Date: 2024-01-01 DOI: 10.1080/19420889.2024.2373301
Arunvel Thangamani, Deepavalli Arumuganainar

As every life form is composed of cells, elements of consciousness, namely memory and sentience, must be grounded in mechanisms that are integral to unicellular organisms. Earlier studies indicated that cellular cytoskeletal structures consisting of excitable, flexible, and oscillating polymers such as microtubules, along with quantum events, are potentially responsible for information processing and thus consciousness. This work attempts to solve the unknown, that is, how, at the spark of life, the phenomenon of cellular information processing first appears. This study posits that the spatially distributed wave energy of the molecules of an incepting cell interacts with space and generates a rotating bioinformation field, forming a vortex. This vortex, the local energy maximum, whose inbound and outbound energy fluxes represent signal reception and dispersal, is a critical step in the spark of life responsible for information storage, and with incremental wave superpositions, exhibits information processing. The vorticity of the rotating field is computed, and the obtained field characteristics indicated the emergence of a prebiotic complex to initiate information processing. Furthermore, the developed system model explains how perturbations from the environment are converted into response signals for the emanation of sense, locomotion, nutrition, and asexual reproduction, the fundamental evolutionary building blocks of prokaryotes. Further research directions include explaining how the energy potential available in the bio-information field and the vortex leads to the first formation of genetic material, emergence of cytoskeleton, and extension of bio-information field to multi-cellular organisms.

由于每种生命形式都是由细胞组成的,因此意识的要素,即记忆和知觉,必须建立在单细胞生物不可或缺的机制之上。早先的研究表明,由微管等可兴奋、柔韧和振荡的聚合物组成的细胞骨架结构,以及量子事件,有可能负责信息处理,从而产生意识。这项研究试图解决一个未知的问题,即在生命的火花中,细胞信息处理现象是如何首次出现的。这项研究认为,萌发细胞的分子在空间分布的波能与空间相互作用,产生了旋转的生物信息场,形成了一个漩涡。这个漩涡是局部能量的最大值,其进出的能量通量代表信号的接收和传播,是生命火花中负责信息存储的关键步骤,并通过增量波叠加展示信息处理。计算了旋转磁场的涡度,获得的磁场特征表明出现了启动信息处理的前生物复合体。此外,所建立的系统模型还解释了来自环境的扰动如何转化为反应信号,从而产生感知、运动、营养和无性繁殖等原核生物的基本进化构件。进一步的研究方向包括解释生物信息场和漩涡中的能量势如何导致遗传物质的首次形成、细胞骨架的出现以及生物信息场如何扩展到多细胞生物。
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引用次数: 0
Identification and selection of reference genes for analysis of gene expression by quantitative real-time PCR in the euhalophyte Suaeda altissima (L.) Pall. 鉴定和选择参考基因,用于通过实时定量 PCR 分析海藻 Suaeda altissima (L.) Pall.
Q2 Agricultural and Biological Sciences Pub Date : 2024-07-08 eCollection Date: 2024-01-01 DOI: 10.1080/19420889.2024.2372313
Dmitrii E Khramov, Olga I Nedelyaeva, Alena O Konoshenkova, Vadim S Volkov, Yurii V Balnokin

Сoding sequences of seven housekeeping genes: actin SaACT7, ubiquitin-conjugating protein SaUBC10, glyceraldehyde-3-phosphate dehydrogenase SaGAPDH, protein of the large subunit of ribosomes SaL2, α-tubulin SaTUA, translation elongation factor SaeEF1α, and protein phosphatase SaPP2A were identified as candidate reference genes for expression analysis of target genes in the extremely salt tolerant plant Suaeda altissima (L.) Pall. The expression profiles of the genes differed. SaACT7 and SaeEF1α demonstrated the highest expression levels, while the lowest expression levels were found for SaPP2A and SaTUA. SaPP2A and SaeEF1α genes were the most stably expressed at different steady-state salinity levels and different nitrate concentrations in nutrient solutions (NSs). SaL2, SaPP2A, and SaeEF1α genes showed the greatest stability of expression when nitrate was added to nutrient solution of plants grown under conditions of nitrate deficiency. Less constant expression was demonstrated in this experiment by SaACT7 and SaTUA. SaL2, SaACT7, SaeEF1α, and SaUBC10 genes showed the smallest expression changes under salt shock. To validate the use of the most stably expressed genes for normalization of gene expression, we checked them as reference genes to study the expression of the nitrate transporter gene SaNPF6.3 in S. altissima roots under conditions of different salinity and different nitrate supply.

确定了七个看家基因的编码序列:肌动蛋白 SaACT7、泛素结合蛋白 SaUBC10、甘油醛-3-磷酸脱氢酶 SaGAPDH、核糖体大亚基蛋白 SaL2、α-微管蛋白 SaTUA、翻译延伸因子 SaeEF1α 和蛋白磷酸酶 SaPP2A,作为候选参考基因,用于分析极耐盐植物 Suaeda altissima (L.) Pall.中靶基因的表达。) Pall.这些基因的表达谱各不相同。SaACT7 和 SaeEF1α 的表达水平最高,而 SaPP2A 和 SaTUA 的表达水平最低。SaPP2A和SaeEF1α基因在不同稳态盐度水平和营养液(NSs)中不同硝酸盐浓度下的表达最为稳定。在硝酸盐缺乏条件下生长的植物的营养液中加入硝酸盐时,SaL2、SaPP2A 和 SaeEF1α 基因的表达最为稳定。在本实验中,SaACT7 和 SaTUA 的表达不太稳定。在盐休克条件下,SaL2、SaACT7、SaeEF1α 和 SaUBC10 基因的表达变化最小。为了验证使用表达最稳定的基因对基因表达进行归一化,我们将它们作为参考基因,研究了不同盐度和不同硝酸盐供应条件下 S. altissima 根中硝酸盐转运体基因 SaNPF6.3 的表达情况。
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引用次数: 0
Microbial communities in the Dead Sea and their potential biotechnological applications. 死海中的微生物群落及其潜在的生物技术应用。
Q2 Agricultural and Biological Sciences Pub Date : 2024-06-23 eCollection Date: 2024-01-01 DOI: 10.1080/19420889.2024.2369782
Hala I Al-Daghistani, Sima Zein, Manal A Abbas

The Dead Sea is unique compared to other extreme halophilic habitats. Its salinity exceeds 34%, and it is getting saltier. The Dead Sea environment is characterized by a dominance of divalent cations, with magnesium chloride (MgCl2) levels approaching the predicted 2.3 M upper limit for life, an acidic pH of 6.0, and high levels of absorbed ultraviolet radiation. Consequently, only organisms adapted to such a polyextreme environment can survive in the surface, sinkholes, sediments, muds, and underwater springs of the Dead Sea. Metagenomic sequence analysis and amino acid profiling indicated that the Dead Sea is predominantly composed of halophiles that have various adaptation mechanisms and produce metabolites that can be utilized for biotechnological purposes. A variety of products have been obtained from halophilic microorganisms isolated from the Dead Sea, such as antimicrobials, bioplastics, biofuels, extremozymes, retinal proteins, colored pigments, exopolysaccharides, and compatible solutes. These resources find applications in agriculture, food, biofuel production, industry, and bioremediation for the detoxification of wastewater and soil. Utilizing halophiles as a bioprocessing platform offers advantages such as reduced energy consumption, decreased freshwater demand, minimized capital investment, and continuous production.

与其他极端嗜卤生境相比,死海是独一无二的。死海的盐度超过 34%,而且还在不断升高。死海环境的特点是二价阳离子占主导地位,氯化镁(MgCl2)含量接近预测的 2.3 M 生命上限,酸性 pH 值为 6.0,紫外线辐射吸收量大。因此,只有适应这种多极端环境的生物才能在死海的地表、水坑、沉积物、泥浆和水下泉水中生存。元基因组序列分析和氨基酸分析表明,死海主要由具有各种适应机制的嗜卤生物组成,它们产生的代谢物可用于生物技术目的。从死海分离出来的嗜卤微生物已经产生了多种产品,如抗菌剂、生物塑料、生物燃料、极端酶、视网膜蛋白、有色色素、外多糖和相容性溶质。这些资源可应用于农业、食品、生物燃料生产、工业以及用于废水和土壤解毒的生物修复。利用嗜卤生物作为生物加工平台具有降低能耗、减少淡水需求、最大限度地减少资本投资和连续生产等优势。
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引用次数: 0
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