Effects of temperature and salinity on Vibrio cholerae growth.

Laboratory microecosystems (microcosms) prepared with a chemically defined sea salt solution were used to study effects of selected environmental parameters on growth and activity of Vibrio cholerae. Growth responses under simulated estuarine conditions of 10 strains of V. cholerae, including clinical and environmental isolates as well as serovars O1 and non-O1, were compared, and all strains yielded populations of approximately the same final size. Effects of salinity and temperature on extended survival of V. cholerae demonstrated that, at an estuarine salinity (25%) and a temperature of 10 degrees C, V. cholerae survived (i.e., was culturable) for less than 4 days. Salinity was also found to influence activity, as measured by uptake of 14C-amino acids. Studies on the effect of selected ions on growth and activity of V. cholerae demonstrated that Na+ was required for growth. The results of this study further support the status of V. cholerae as an estuarine bacterium.     

Kin interactions and changing social structure during a population outbreak of feral house mice

Populations of feral house mice (Mus domesticus L.) in Australia undergo multiannual fluctuations in density, and these outbreaks may be partly driven by some change in behavioural self-regulation. In other vertebrate populations with multiannual fluctuations, changes in kin structure have been proposed as a causal mechanism for changes in spacing behaviour, which consequently result in density fluctuations. We tested the predictions of two alternative conceptual models based on kin selection in a population of house mice during such an outbreak. Both published models (Charnov & Finerty 1980; Lambin & Krebs 1991) propose that the level of relatedness between interacting individuals affects their behavioural response and that this changes with population density, though the nature of this relationship differs between the two models. Neither of the models was consistent with all observed changes in relatedness between interacting female mice; however, our results suggested that changes in kin structure still have potential for explaining why mouse outbreaks begin. Therefore, we have developed a variant of one of these conceptual models suggesting that the maintenance of female kin groups through the preceding winter significantly improves recruitment during the subsequent breeding season, and is therefore necessary for mouse outbreaks. We provide six testable predictions to falsify this hypothesis.     

Measures of Autozygosity in Decline: Globalization, Urbanization, and Its Implications for Medical Genetics

This research investigates the influence of demographic factors on human genetic sub-structure. In our discovery cohort, we show significant demographic trends for decreasing autozygosity associated with population variation in chronological age. Autozygosity, the genomic signature of consanguinity, is identifiable on a genome-wide level as extended tracts of homozygosity. We identified an average of 28.6 tracts of extended homozygosity greater than 1 Mb in length in a representative population of 809 unrelated North Americans of European descent ranging in chronological age from 19–99 years old. These homozygous tracts made up a population average of 42 Mb of the genome corresponding to 1.6% of the entire genome, with each homozygous tract an average of 1.5 Mb in length. Runs of homozygosity are steadily decreasing in size and frequency as time progresses (linear regression, p<0.05). We also calculated inbreeding coefficients and showed a significant trend for population-wide increasing heterozygosity outside of linkage disequilibrium. We successfully replicated these associations in a demographically similar cohort comprised of a subgroup of 477 Baltimore Longitudinal Study of Aging participants. We also constructed statistical models showing predicted declining rates of autozygosity spanning the 20th century. These predictive models suggest a 14.0% decrease in the frequency of these runs of homozygosity and a 24.3% decrease in the percent of the genome in runs of homozygosity, as well as a 30.5% decrease in excess homozygosity based on the linkage pruned inbreeding coefficients. The trend for decreasing autozygosity due to panmixia and larger effective population sizes will likely affect the frequency of rare recessive genetic diseases in the future. Autozygosity has declined, and it seems it will continue doing so.     

Metal cation uptake by yeast: a review

This review addresses metal uptake specifically by yeast. Metal uptake may be passive, active or both, depending on the viability of the biomass, and is influenced by a number of environmental and experimental factors. Uptake is typically accompanied by a degree of ion exchange and, under certain conditions, may be enhanced by the addition of an energy source, Intracellularly accumulated metal is most readily associated with the cell wall and vacuole but may also be bound by other cellular organelles and biomolecules. The intrinsic biochemical, structural and genetic properties of the yeast cell along with environmental conditions are crucial for its survival when exposed to toxic metals. Conditions of pH, temperature and the presence of additional ions, amongst others, have varying effects on the metal uptake process. We conclude that yeasts have contributed significantly to our understanding of the metal uptake process and suggest directions for future work.     

Robustness and innovation along the endocytic route: Lessons from darkness

What mechanisms ensure the loading of a SNARE into a nascent carrier? In this issue, Bowman et al. (2021. J. Cell Biol. https://doi.org/10.1083/jcb.202005173) describe an unprecedented mechanism where two sorting complexes, AP-3 and BLOC-1, the latter bound to syntaxin 13, work as a fail-safe to recognize sorting signals in VAMP7, a membrane protein required for fusion to melanosomes. Their observations define one of the first examples of distributed robustness in membrane traffic mechanisms.

Eukaryotic cells are defined by a complex collection of membrane-bound organelles, each with their unique catalog of constituents, such as membrane proteins. A precise repertoire of membrane proteins is necessary for these organelles to function properly. Membrane proteins selectively populating either melanosomes (or any other endomembrane organelle) originate in the endoplasmic reticulum and travel to their final destination. This observation raised one of the most fundamental questions in cell biology: how do all membrane proteins reach their diverse destinations despite being born in the same place, the endoplasmic reticulum? The answer has been in the making for ∼60 yr.The prevailing model considers that membrane and soluble proteins in the lumen of organelles are selectively loaded at the donor membrane into membrane-bound carriers of vesicular or tubular nature. Selective cargo loading is accomplished by cytoplasmic protein complexes that sort these complexes into a nascent carrier (1). In this issue, Bowman et al. (2) focused on two sorting complexes, the adaptor complex adaptor protein-3 (AP-3) and biogenesis of lysosome-related organelles complex (BLOC)-1 complex (3). Once formed, membrane-bound carriers must fuse with their target organelle to deliver their content (1). The fusion step is controlled by a complex machinery centered around fusogenic membrane proteins known as SNAREs. SNAREs must be sorted into a carrier (R-SNAREs) in order to be competent for fusion (1). Preventing an R-SNARE from loading into its carrier impairs carrier fusion with the target membrane and results in dramatic consequences for cells and organisms. For example, removal of the R-SNARE from carriers bound to melanosomes generates melanosomes that fail to produce pigment, a cellular phenotype used by Bowman et al. (2). In the case of synaptic vesicles, elimination of R-SNAREs from these vesicles prevents their fusion with the plasmalemma halting neurotransmission with overt manifestations such as paralysis (4). Thus, any carrier without an R-SNARE is a cellular and organismal catastrophe.How does a carrier acquire its SNARE in order to deliver their content to a donor compartment? So far, the model has been one of binary interactions between a SNARE signal and a sorting complex that recognizes that signal (5). These binary interactions can be tested by either mutagenesis of the SNARE signal or the domain in the sorting complex that binds the SNARE signal. Either one of these experimental manipulations results in SNARE depletion from the target membrane and defective function of the target organelle. But what happens when the disruption of a binary interaction does not reveal any of the expected phenotypes? Frequently, such outcomes are explained away by an unidentified, speculative, and unattractive redundancy within the system. Bowman et al. take the long and winding road of identify the source of the so-called “redundancy” in the delivery of an R-SNARE vesicle-associated membrane protein 7 (VAMP7) to melanosomes. VAMP7 travels from endosomes (the donor compartment) to the melanosome (the target compartment) via tubules. VAMP7 concentrates in these tubules by a tripartite process established by a super-complex made by AP-3, BLOC-1, and syntaxin 13. VAMP7 is loaded into these tubules either because AP-3 sorts VAMP7 by direct binding or because BLOC-1 sorts VAMP7 into the same tubule using the VAMP7-binding property of syntaxin 13. Here syntaxin 13, a target or Q-SNARE, moonlights in this mechanism as an “accessory adaptor” linking VAMP7 to BLOC-1. Importantly, there is no role for syntaxin 13 as a SNARE in the fusion of tubules to melanosomes (6). Bowman et al. expose defects in pigmentation and cargo delivery from endosomes to melanosomes (the catastrophe) only when the interactions of AP-3 with VAMP7 and BLOC-1 with syntaxin 13 are simultaneously abrogated by mutagenesis. These experiments elegantly reveal the identity of the fail-safe mechanism in VAMP7 sorting to melanosomes.If carriers without R-SNARE lead to catastrophic failures, what are the fail-safe mechanisms built in the R-SNARE loading step? Redundancy of components can be seen as biology’s engineering approach to build fail-safe systems. The capacity to withstand disruption defines a system’s robustness (7, 8). If the loading of an R-SNARE into a vesicle is a critical step in any trafficking event, it is reasonable to ask how cells build a system that assures R-SNARE loading into carriers. One such approach comes in the form of several paralog R-SNAREs loaded on a vesicle by their cognate sorting complex, such as in synaptic vesicles, coat protein complex II, or clathrin-coated vesicles (4, 9, 10, 11, 12). In these cases, different SNAREs bind to their dedicated sorting molecule following a binary mechanism. This represents a robustness built by copies of the same type of entities, much like the two-parachute fail-safe approach in skydiving. In contrast, Bowman et al. present the first example where the system’s resilience is built by two dissimilar strategies acting on the same R-SNARE (2). This would be analogous to replacing one of the two parachutes with a jet pack during skydiving. Such systems where robustness is built by dissimilar strategies are known as systems with distributed robustness. While distributed robustness is well known in the organization of metabolic networks and developmental mechanisms, to the best of our knowledge this is a one-of-a-kind example in membrane traffic mechanisms (7, 8).Robust systems tolerate transient variation, such as environmental variation, but more importantly, robust systems can buffer permanent modifications, including genetic variation, keeping the system away from catastrophe (7, 8). Buffered genetic variation could contribute to noncatastrophic phenotypic variation, opening the door for intermediate phenotypes to emerge in the short term (7, 8). For example, melanosomes contributing to degrees of tanning caused seasonal variations on skin UV light exposure. However, buffered genetic variation could contribute to potential future phenotypic evolution in the long run (7, 8). This last contribution of robustness could open the door for the appearance of cell type–specific membrane traffic mechanisms and the emergence of novel organelles, such as the melanosome. In addition, a robust melanosome biogenesis system could be permissive for the evolution of fur colors selectable by the environment. This is the case of beach mice where allelic variation in one gene contributes to the emergence of adaptive beach mouse color patterns (Fig. 1; 13, 14). While these ideas are speculative, the excitement of Bowman et al.’s work is that they invite us to think beyond the immediacy of the process they studied. Their elegant findings suggest conceptual novelty in membrane traffic in the form of distributed robustness. The idea of distributed robustness may become a cell trafficking principle waiting to be revealed by à la Bowman experimentation.Open in a separate windowFigure 1.Variation of fur color among beach mice. Diagram shows the geographic distribution of the beach mouse Peromyscus polionotus. Brown shading represents the habitat of mainland subspecies. Color variation is attributed to allelic variation in one gene involved in melanosome pigmentation. The figure is reproduced from Steiner et al. (14) with permission of Oxford University Press, and abbreviations in parentheses designate subspecies as described by the authors. PPSm, P. polionotus sumneri; PPP, P. p. polionotus; PPSu, P. p. subgriseus.     

Ecological Indicators of Native Rhizobia in Tropical Soils

The relationship between environment and abundance of rhizobia was described by determining the populations of root nodule bacteria at 14 diverse sites on the island of Maui. Mean annual rainfall at the sites ranged from 320 to 1,875 mm, elevation from 37 to 1,650 m, and soil pH from 4.6 to 7.9. Four different soil orders were represented in this study: inceptisols, mollisols, ultisols, and an oxisol. The rhizobial populations were determined by plant infection counts of five legumes (Trifolium repens, Medicago sativa, Vicia sativa, Leucaena leucocephala, and Macroptilium atropurpureum). Populations varied from 1.1 to 4.8 log₁₀ cells per g of soil. The most frequently occurring rhizobia were Bradyrhizobium spp., which were present at 13 of 14 sites with a maximum of 4.8 log₁₀ cells per g of soil. Rhizobium trifolii and R. leguminosarum occurred only at higher elevations. The presence of a particular Rhizobium or Bradyrhizobium sp. was correlated with the occurrence of its appropriate host legume. Total rhizobial populations were significantly correlated with mean annual rainfall, legume cover and shoot biomass, soil temperature, soil pH, and phosphorus retention. Regression models are presented which describe the relationship of legume hosts, soil climate, and soil fertility on native rhizobial populations.     

Improved Assay for Rhodanese in Thiobacillus spp

Rhodanese (thiosulfate:cyanide sulfurtransferase; EC 2.8.1.1) catalyzes the conversion of thiosulfate and cyanide to thiocyanate and sulfite. Conventional rhodanese assays colorimetrically measure the formation of one or the other of the products. These assays suffer from the fact that there is significant nonbiological formation of these products in addition to the enzymatically catalyzed reaction. In the present report, we describe a modified procedure for assaying rhodanese in which a separate boiled control was prepared for each assay trial. The boiled control corrected for the nonbiological contributions to product formation.     

Influence of the Size of Indigenous Rhizobial Populations on Establishment and Symbiotic Performance of Introduced Rhizobia on Field-Grown Legumes

Indigenous rhizobia in soil present a competition barrier to the establishment of inoculant strains, possibly leading to inoculation failure. In this study, we used the natural diversity of rhizobial species and numbers in our fields to define, in quantitative terms, the relationship between indigenous rhizobial populations and inoculation response. Eight standardized inoculation trials were conducted at five well-characterized field sites on the island of Maui, Hawaii. Soil rhizobial populations ranged from 0 to over 3.5 × 10⁴ g of soil^-1 for the different legumes used. At each site, no less than four but as many as seven legume species were planted from among the following: soybean (Glycine max), lima bean (Phaseolus lunatus), cowpea (Vigna unguiculata), bush bean (Phaseolus vulgaris), peanut (Arachis hypogaea), Leucaena leucocephala, tinga pea (Lathyrus tingeatus), alfalfa (Medicago sativa), and clover (Trifolium repens). Each legume was (i) inoculated with an equal mixture of three effective strains of homologous rhizobia, (ii) fertilized at high rates with urea, or (iii) left uninoculated. For soybeans, a nonnodulating isoline was used in all trials as the rhizobia-negative control. Inoculation increased economic yield for 22 of the 29 (76%) legume species-site combinations. While the yield increase was greater than 100 kg ha^-1 in all cases, in only 11 (38%) of the species-site combinations was the increase statistically significant (P ≤ 0.05). On average, inoculation increased yield by 62%. Soybean (G. max) responded to inoculation most frequently, while cowpea (V. unguiculata) failed to respond in all trials. Inoculation responses in the other legumes were site dependent. The response to inoculation and the competitive success of inoculant rhizobia were inversely related to numbers of indigenous rhizobia. As few as 50 rhizobia g of soil^-1 eliminated inoculation response. When fewer than 10 indigenous rhizobia g of soil^-1 were present, economic yield was significantly increased 85% of the time. Yield was significantly increased in only 6% of the observations when numbers of indigenous rhizobia were greater than 10 cells g of soil^-1. A significant response to N application, significant increases in nodule parameters, and greater than 50% nodule occupancy by inoculant rhizobia did not necessarily coincide with significant inoculation responses. No less than a doubling of nodule mass and 66% nodule occupancy by inoculant rhizobia were required to significantly increase the yield of inoculated crops over that of uninoculated crops. However, lack of an inoculation response was common even when inoculum strains occupied the majority of nodules. In these trials, the symbiotic yield of crops was, on average, only 88% of the maximum yield potential, as defined by the fertilizer N treatment. The difference between the yield of N-fertilized crops and that of N₂-fixing crops indicates a potential for improving inoculation technology, the N₂ fixation capacity of rhizobial strains, and the efficiency of symbiosis. In this study, we show that the probability of enhancing yield with existing inoculation technology decreases dramatically with increasing numbers of indigenous rhizobia.     

Modeling Symbiotic Performance of Introduced Rhizobia in the Field by Use of Indices of Indigenous Population Size and Nitrogen Status of the Soil

The ability to predict the symbiotic performance of rhizobia introduced into different environments would allow for a more judicious use of rhizobial inoculants. Data from eight standardized field inoculation trials were used to develop models that could be used to predict the success of rhizobial inoculation in diverse environments based on indices of the size of indigenous rhizobial populations and the availability of mineral N. Inoculation trials were conducted at five diverse sites on the island of Maui, Hawaii, with two to four legumes from among nine species, yielding 29 legume-site observations. The sizes of indigenous rhizobial populations were determined at planting. Soil N mineralization potential, total soil N, N accumulation and seed yield of nonnodulating soybean, and N derived from N₂ fixation in inoculated soybean served as indices of available soil N. Uninoculated, inoculated, and fertilizer N treatments evaluated the impact of indigenous rhizobial populations and soil N availability on inoculation response and crop yield potential. The ability of several mathematical models to describe the inverse relationship between numbers of indigenous rhizobia and legume inoculation responses was evaluated. Power, exponential, and hyperbolic functions yielded similar results; however, the hyperbolic equation provided the best fit of observed to estimated inoculation responses (r² = 0.59). The fact that 59% of the observed variation in inoculation responses could be accounted for by the relationship of inoculation responses to numbers of indigenous rhizobia illustrates the profound influence that the size of soil rhizobial populations has on the successful use of rhizobial inoculants. In the absence of indigenous rhizobia, the inoculation response was directly proportional to the availability of mineral N. Therefore, the hyperbolic response function was subsequently combined with several indices of soil N availability to generate models for predicting legume inoculation response. Among the models developed, those using either soil N mineralization potential or N derived from N₂ fixation in soybean to express the availability of mineral N were most useful in predicting the success of legume inoculation. Correlation coefficients between observed and estimated inoculation responses were r = 0.83 for the model incorporating soil N mineralization potential and r = 0.96 for the model incorporating N derived from N₂ fixation. Several equations collectively termed “soil N deficit factors” were also found to be useful in estimating inoculation responses. In general, models using postharvest indices of soil N were better estimators of observed inoculation responses than were those using laboratory measures of soil N availability. However, the latter, while providing less precise estimates, are more versatile because all input variables can be obtained through soil analysis prior to planting. These models should provide researchers, as well as regional planners, with a more precise predictive capability to determine the inoculation requirements of legumes grown in diverse environments.