Rare Members Research Articles

Diversity of Oomycetes From Alabama Cotton Soils Using Culture-Independent Methods.

Seedling disease management recommendations rely on comprehensive identification of the pathogens. A recent manuscript isolated oomycetes from diseased cotton (Gossypium hirsutum L.) roots to identify the species associated. However, culture-dependent surveys may miss species because of the microbiological medium and work required to isolate and maintain all cultured organisms. Alternatively, culture-independent methods using PCR amplification and high-throughput sequencing can identify species' presence and relative abundance, including obligate pathogens and rare members of communities. We used culture-independent sequencing from the same cotton soils in the culture-based survey to determine the oomycete species in oomycete-containing soils. The results of the two methods were generally similar regarding the species identified. Similarly to the culture-based method, Globisporangium irregular accounted for 24% of the relative abundance and was encountered in all fields sequenced. In contrast, we identified three operational taxonomic units matching Globisporangium ultimum, but accounted for less than 0.06% of total relative abundance, potentially explaining why it was not isolated from cotton roots in the original survey. Phytophthora nicotianae was identified in soils but not at the concentrations recorded in the culture-based study. The results of this study, combined with the results of the culture-based survey, demonstrate the most comprehensive identification of oomycetes associated with cotton in the cotton belt and the oomycetes related to seedling disease. The combined results will be essential for future research into the specific pathogen species mentioned and stimulate similar research in other states.

Metapresence: a tool for accurate species detection in metagenomics based on the genome-wide distribution of mapping reads.

Shotgun metagenomics allows comprehensive sampling of the genomic information of microbes in a given environment and is a tool of choice for studying complex microbial systems. Mapping sequencing reads against a set of reference or metagenome-assembled genomes is in principle a simple and powerful approach to define the species-level composition of the microbial community under investigation. However, despite the widespread use of this approach, there is no established way to properly interpret the alignment results, with arbitrary relative abundance thresholds being routinely used to discriminate between present and absent species. Such an approach can be affected by significant biases, especially in the identification of rare species. Therefore, it is important to develop new metrics to overcome these biases. Here, we present Metapresence, a new tool to perform reliable identification of the species in metagenomic samples based on the distribution of mapped reads on the reference genomes. The analysis is based on two metrics describing the breadth of coverage and the genomic distance between consecutive reads. We demonstrate the high precision and wide applicability of the tool using data from various synthetic communities, a real mock community, and the gut microbiome of healthy individuals and antibiotic-associated-diarrhea patients. Overall, our results suggest that the proposed approach has a robust performance in hard-to-analyze microbial communities containing contaminated or closely related genomes in low abundance.IMPORTANCEDespite the prevalent use of genome-centric alignment-based methods to characterize microbial community composition, there lacks a standardized approach for accurately identifying the species within a sample. Currently, arbitrary relative abundance thresholds are commonly employed for this purpose. However, due to the inherent complexity of genome structure and biases associated with genome-centric approaches, this practice tends to be imprecise. Notably, it introduces significant biases, particularly in the identification of rare species. The method presented here addresses these limitations and contributes significantly to overcoming inaccuracies in precisely defining community composition, especially when dealing with rare members.

Observations on the Vegetation of Eastern Kumaon Bordering the Nepal Frontier

The paper describes some of the observations made during a botanical exploration tour of Eastern Kumaon bordering the Nepal Frontier and includes a list of plants collected with brief botanical notes. Among the plants collected are specimens of Triosteum hirsutum Wall., a rare member of Caprifoliaceae, Stylophorum lactucoides Benth. & Hook. f. of the Papaveraceae rarely collected in the past, Osmunda regalis L. and Thesium himalense Royle.

Abstract PO1-21-01: A Case of High Grade Metastatic Encapsulated Papillary Carcinoma and a Look at Current Treatment Guidelines

Abstract Background: Encapsulated papillary carcinoma is a well-documented malignancy in the world of breast surgery. It is often described as a less invasive form of breast cancer, with a more indolent clinical course. Most EPC pathology demonstrates low grade tumors, with rare findings of metastases at time of diagnosis. EPC currently accounts for 1-2% of all breast cancers. It is distinguished by its fibrovascular core, which is covered with epithelium with or without a myoepithelial layer. Despite EPC being well-recognized, current management remains controversial. Most commonly, however, it is treated and managed as an in-situ disease. Case Presentation: We present a case of a 64-year-old female who initially presented with a painless lump in her left breast, which on biopsy demonstrated DCIS involved with a papillary lesion. On excision, the patient was upstaged to IDC in a background of EPC. She then underwent re-excision with confirmed negative margins. Despite this, over the following months, the patient continued to have increased pain, swelling, and an episode of superficial thrombophlebitis. She was taken back to the OR at this time and was found to have a new mass with a large feeding vein. Pathology was significant for high grade multifocal EPC with small and large vessel lympho-vascular invasion. Lesion noted to be metachronous. Additionally, metastases to the axilla were identified, requiring an axillary dissection. Conclusion: High grade encapsulated papillary carcinoma is a rare member of the indolent papillary breast cancer family. This unusually invasive type of cancer should be treated and managed in a more aggressive fashion, like its clinically similar cousin invasive ductal carcinoma. The current management standard of treating EPC as in situ disease is not robust enough and can lead to disease recurrence and need for repeat resection and treatment. Citation Format: Nicholas Gore MD, Madeline Silva MD, Carissia Calvo-Strube MD. A Case of High Grade Metastatic Encapsulated Papillary Carcinoma and a Look at Current Treatment Guidelines [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO1-21-01.

Unveiling the culturable and non-culturable actinobacterial diversity in two macroalgae species from the northern Portuguese coast.

Actinomycetota, associated with macroalgae, remains one of the least explored marine niches. The secondary metabolism of Actinomycetota, the primary microbial source of compounds relevant to biotechnology, continues to drive research into the distribution, dynamics, and metabolome of these microorganisms. In this study, we employed a combination of traditional cultivation and metagenomic analysis to investigate the diversity of Actinomycetota in two native macroalgae species from the Portuguese coast. We obtained and taxonomically identified a collection of 380 strains, which were distributed across 12 orders, 15 families, and 25 genera affiliated with the Actinomycetia class, with Streptomyces making up approximately 60% of the composition. Metagenomic results revealed the presence of Actinomycetota in both Chondrus crispus and Codium tomentosum datasets, with relative abundances of 11% and 2%, respectively. This approach identified 12 orders, 16 families, and 17 genera affiliated with Actinomycetota, with minimal overlap with the cultivation results. Acidimicrobiales emerged as the dominant actinobacterial order in both macroalgae, although no strain affiliated with this taxonomic group was successfully isolated. Our findings suggest that macroalgae represent a hotspot for Actinomycetota. The synergistic use of both culture-dependent and independent approaches proved beneficial, enabling the identification and recovery of not only abundant but also rare taxonomic members.

Bacterial communities of planktonic bacteria and mature biofilm in service lines and premise plumbing of a Megacity: Composition, Diversity, and influencing factors

Although simulated studies have provided valuable knowledge regarding the communities of planktonic bacteria and biofilms, the lack of systematic field studies have hampered the understanding of microbiology in real-world service lines and premise plumbing. In this study, the bacterial communities of water and biofilm were explored, with a special focus on the lifetime development of biofilm communities and their key influencing factors. The 16S rRNA gene sequencing results showed that both the planktonic bacteria and biofilm were dominated by Proteobacteria. Among the 15,084 observed amplicon sequence variants (ASVs), the 33 core ASVs covered 72.8 %, while the 12 shared core ASVs accounted for 62.2 % of the total sequences. Remarkably, it was found that the species richness and diversity of biofilm communities correlated with pipe age. The relative abundance of ASV2 (f_Sphingomonadaceae) was lower for pipe ages 40–50 years (7.9 %) than for pipe ages 10–20 years (59.3 %), while the relative abundance of ASV10 (f_Hyphomonadaceae) was higher for pipe ages 40–50 years (19.5 %) than its presence at pipe ages 20–30 years (1.9 %). The community of the premise plumbing biofilm had significantly higher species richness and diversity than that of the service line, while the steel-plastics composite pipe interior lined with polyethylene (S-PE) harbored significantly more diverse biofilm than the galvanized steel pipes (S-Zn). Interestingly, S-PE was enriched with ASV27 (g_Mycobacterium), while S-Zn pipes were enriched with ASV13 (g_Pseudomonas). Moreover, the network analysis showed that five rare ASVs, not core ASVs, were keystone members in biofilm communities, indicating the importance of rare members in the function and stability of biofilm communities. This manuscript provides novel insights into real-world service lines and premise plumbing microbiology, regarding lifetime dynamics (pipe age 10–50 years), and the influences of pipe types (premise plumbing vs. service line) and pipe materials (S-Zn vs. S-PE).

18F-FDG PET/CT Imaging for Treatment Response Assessment of Cardiac Primitive Neuroectodermal Tumor.

Primitive neuroectodermal tumors (PNETs) are rare and aggressive members of the small round cell carcinoma family. Generally, PNETs are classified into two main groups: PNETs of the central nervous system and PNETs of the peripheral nervous system. Herein, we report the therapy response assessment of a rare case of isolated cardiac PNET using 18F-fluorodeoxyglucose (18F-FDG) positron emission tomography/computed tomography (PET/CT) imaging. Given that physiological cardiac FDG uptake is typically observed, assessing FDG avid lesions in the myocardium presents a challenge for FDG PET/CT. This case holds significance because of the rarity of the disease and the challenging nature of the site for FDG PET/CT imaging.

Phyllosphere to Ferment: Site Conditions Structure Cacao Pod and Fermentation Microbiomes in Hawaiʻi

Microbial fermentation is crucial to the development of flavors in cacao-based products, but how the abiotic environment and pod surface microbiomes can contribute to these different sensory profiles is underdeveloped. To better understand the connections between environment, plant variety, associated pod phyllosphere microbiomes, and the fermentation microbiome, we characterized the fungi and bacteria on pod surfaces and early fermentations of two cacao varieties across wet and dry sites on the island of O‘ahu, Hawai‘i. We showed that site (and the environmental conditions linked to those sites) significantly influenced the microbiomes of both the pod phyllosphere and fermentations but did not significantly explain the differences between cacao varieties. Certain taxa of bacteria and fungi seemingly prefer the wet Kualoa Ranch site compared with the drier Urban Garden Center Site. Rare members of the pod phyllosphere communities became highly enriched during fermentation, where basidiomycetous yeasts ( Filobasidium sp., Hannaella zeae, Rhodotorula mucilaginosa, R. paludigena, and Sporobolomyces carnicolor) became dominant at the wet site, and both ascomycetous and basidiomycetous yeasts ( Hyphopichia burtonii, Meyerozyma sp., Yamadazyma phyllophila, Filobasidium sp., Kwoniella heveanensis, R. mucilaginosa, Sporobolomyces sp., and S. carnicolor) became dominant at the dry site. The agricultural production site where cacao plants are grown should be considered carefully because it is likely important in structuring microbes that are present on pod surfaces and the microbes (mostly yeasts) that will be carried forward into fermentation. These yeasts may contribute to the development of the unique fruity or floral flavors in chocolates produced in Hawai‘i. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Developing a community-led rare disease ELSI research agenda.

Research priorities are best defined through engagement with communities who will be impacted by the research and have lived experience of the topics to be studied. We aimed to establish a pediatric rare disease community stakeholder group and empower them in (1) eliciting perspectives from affected families in the wider region and (2) synthesizing collective ideas into a research agenda focused on shared ethical, legal, and social implications (ELSI) across rare disease. This two-year project utilized a community-centered approach to engage rare disease community members as equal partners in developing a research agenda for ELSI in rare disease. We established "Rare Voices" (RV), a 22-member stakeholder group of patients, parents, clinicians and researchers. Following capacity-building trainings, RV designed and conducted listening sessions with teen patients and parents of children with rare diseases to explore challenges, positive experiences, and ethical concerns. Listening session findings were synthesized and contextualized into research topics, which RV members further refined and prioritized. We used established measures to assess RV member engagement and satisfaction. From 14 listening sessions with parents (n = 52) and teen patients (n = 13), RV identified eight core research topics as most important for future rare disease research: coordinating care, communication, accessing resources and care, impact on family unit, community and support in society, mental health and identity, ethical aspects of care, and uncertainty. RV members were highly engaged throughout the two-year project and reported high levels of satisfaction with the experience and research agenda. Through capacity-building and authentic engagement, this project resulted in a community-led rare disease research agenda to guide future rare disease ELSI research that aligns with patients' and families' priorities. An environment of equal partnership and respect created a space for mutual learning where community members were empowered to shape the research agenda based on their collective experiences. The agenda recognizes the shared psychosocial and healthcare experiences of rare disease and offers practical areas of research to address patient and family needs.

An intermediate member of the scorodite - strengite series, scorodite56 - strengite41, from Kutná hora ore district, Czech Republic: chemistry and X-ray powder diffraction study

A rare intermediate member of the scorodite - strengite series with an extraordinarily high degree of the anionic P for As substitution, technically a scorodite extremely rich in phosporus, scorodite56 - strengite41 (Scd56 - Stg41), was found and identified from mine dump material of the Rejzské pásmo Lode of the Kutná Hora ore district, Czech Republic. The mineral forms fine-grained, light brownish yellow crystalline masses and coatings, several milimeters in thickness on areas of tens of cm2 on the surface of drusy quartz gangue with partially corroded galena and arsenopyrite. Chemical analyses revealed substantial amount of anionic phosphorus substituting for arsenic, ranging from 39.0 to 44.1 at. % of P (mean 41.0 %). Its chemical composition (mean of nine point analyses) corresponds to the empirical formula (Fe3+0.93Al0.03Pb0.01)Σ0.97[(As0.56P0.41S0.03)Σ1.00O4.00]·2H2O. Such a scope of the P for As substitution in members of the scorodite - strengite series is rare and exceptional. X-ray powder diffraction data, unit-cell parameters and space group for the intermediate member are reported [a = 8.844(2) Å, b = 9.969(2) Å, c = 10.247(2) Å, unit-cell volume V = 903.39 Å3, Z = 8 and space group Pbca]. No discontinuation of the solid solution between scorodite and strengite has been observed, X-ray powder difraction analysis unambiguously confirmed the existence of a single phase representing an intermediate member.

Nadir İki Ascomycota Üyesi İçin Türkiye’de Yeni Lokalite Kayıtları

Apothecia of two previously reported rare members of Ascomycota, Dumontinia tuberosa and Sarcopeziza sicula, were collected from different localities and identified. Dumontinia tuberosa was collected from the Eastern Black Sea Region while S. sicula was collected from Central Anatolian and Southeastern Anatolian Regions of Türkiye. Brief descriptions and new distribution localities of the species were provided together with the photographs of their macro and micromorphologies.

Stakeholder Perceptions of Complementary and Integrative Medicines from People Living with Rare Diseases in Northern Ireland: A Mixed Methods Study

Introduction: Only 5% of rare diseases have an approved treatment available, therefore patients often utilise complementary and integrative medicines (CIMs) to help manage their condition. Limited high-quality evidence-based studies are available which support the effectiveness of CIM, as it is difficult to show that an outcome is a direct result of the CIM intervention and not due to bias. Patients and healthcare professionals must weigh up the evidence quality, safety, efficacy, practical logistics, and financial implications of utilising CIM for rare diseases. This study aimed to elucidate perspectives of stakeholders (individuals with rare diseases, carers, family members, CIM practitioners and healthcare professionals), on the usage of CIM for rare diseases across Northern Ireland. Methods: This was a mixed methods study. An online survey was open from January to February 2019 (n = 29 responses). Themes identified from the survey were then discussed with stakeholders in a semi-structured discussion workshop in March 2019. Results: A limited number of participants responded to the survey (n = 29). Some individuals with rare diseases reported CIM as effective in the management of their condition, in particular acupuncture, dietary supplements, herbal medicines, homoeopathy, hydrotherapy, kinesiology, mindfulness, pilates, reflexology, tai chi, and yoga. However, a number of respondents (n = 7) experienced a negative side effect from CIM. Workshop participants raised concerns over the lack of information available about CIM and rare disease. Both the survey and workshop identified inequality of access with participants reporting CIM to be expensive. Conclusions: More information, high-quality research, and education about CIM are required for patients and healthcare professionals to help make informed decisions about the usage of CIM for rare diseases. Improved communication, information, and health and social care in general would help individuals be more confident and knowledgeable about therapeutic options in relation to their rare disease(s).

Abstract C024: Room temperature stabilization of fecal samples supports important microbiome insights to expand access

Abstract Analysis of microbial signatures associated with colorectal cancer has potential to improve access and adherence to cancer screening programs through non-invasive sampling, particularly in underserved communities. Lack of reproducibility between studies remains a challenge and has limited the ability to translate research findings into scalable clinical applications. The common practice of storing samples at -80°C/-112°F is inconvenient, often not feasible, and may introduce bias if samples are not handled carefully and consistently. Large-scale screening programs would benefit from room temperature stabilization and sample homogenization at the point of collection, without the logistical considerations for rapid and long-term freezing. To evaluate the potential of room temperature stability, fecal samples from adult and pediatric individuals were self-collected at home using the OMNIgene™•GUT Dx device with corresponding unstabilized samples stored at -80°C/-112°F. Metagenomics sequencing was utilized to generate microbiome profiles and identify taxa-associated biomarkers relevant to gastrointestinal health and aging. Stabilized samples were compared to freshly collected unstabilized samples (n=18) to evaluate any bias introduced by the stabilizing solution. The same stabilized samples were compared to unstabilized samples stored at -80°C/-112°F to evaluate stability over time. In addition, reproducibility was evaluated by performing DNA extractions in triplicate from ten stabilized fecal samples. Finally, the ability of the room temperature stabilization to capture expected differences between groups was evaluated by comparing adult and pediatric (n=30 per group) samples and looking for known signatures specific to each group. This research demonstrated equivalent stability over time between stabilized samples at room temperature and unstabilized samples stored at -80°C/-112°F, showing preservation of both highly abundant and rare members of the microbial community. Findings indicate that room temperature stabilization does not introduce bias relative to freshly collected unstabilized samples and produces sufficient sample homogenization to yield reproducible microbial profiles. The comparison between adult and pediatric stabilized fecal samples highlights an enrichment for pediatric-specific signatures, such as Bifidobacterium and Veillonella species, and further captures the lower diversity of pediatric samples relative to more developed adult microbiota. These results demonstrate that the OMNIgene™•GUT Dx device enables the preservation of microbial community structure with room temperature stabilization and sample homogenization for use in the detection of biomarkers in fecal samples. Simple logistics of room temperature storage, combined with an easy-to-use self-collection design and compatibility with standard postal shipping assist integration into clinical workflows and enable at-home collections from diverse populations, especially at-risk, minority populations without easy access to clinical services. Citation Format: Savannah Colameco, Jean M. Macklaim, Ashlee Brown, Tara Crawford Parks. Room temperature stabilization of fecal samples supports important microbiome insights to expand access [abstract]. In: Proceedings of the 16th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2023 Sep 29-Oct 2;Orlando, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2023;32(12 Suppl):Abstract nr C024.

Solutions for optimal care and research for children and adolescents with extremely rare cancers developed within the Joint Action for Rare Cancers (JARC)

Very rare cancers in children and adolescents pose a unique challenge for optimal care and research. Due to their rarity and diversity, there is a lack of standardized treatments and limited data to guide clinical decision-making. This paper aims to provide solutions for addressing these challenges through a multidisciplinary approach involving clinicians, researchers, and patient advocates. In recent years, members of the European Cooperative Study Group for Paediatric Rare Tumors (EXPeRT) and members of the European Society of Pediatric Oncology (SIOPE) clinical council worked within the EU Joint Action on Rare Cancers (JARC) and the Paed Can European Reference Network (ERN) on solutions to improve the care and research in the field. This includes a better classification, more financial resources, higher awareness and support by stakeholders, an international database, as well as harmonized diagnostic and therapeutic guidelines. Further research projects in the field of molecular biology, a better collaboration between medical oncologists and pediatricians, and a general strategy to facilitate access to modern therapies are urgently needed.

Genus <i>Betula</i> L.: Species-Specific Population-Genetic Features and Taxonomy Problems

The article summarizes and systematizes the results of studies by Russian and foreign authors related to the population-genetic features of the main members (silver birch Betula pendula Roth, downy birch Betula pubescens Ehrh, curly (or Karelian) birch Betula pendula Roth var. carelica (Mercklin) Hämet-Ahti) of the birch genus (Betula L.) growing in the forest zone of Europe. Information is provided about forming of birch populations in the region and about its migration pathways when recolonizing the territory after the Ice Age. We demonstrate that due to certain geographic and climatic affiliations there appeared zones of hybridization between different birch species, which had an effect on the subsequent evolution of this genus. Attention is given to the role of hybridization in shaping the genetic structure of the birch population in the north-western part of continental Europe, where introgression has generated unusual genotypes and haplotypes, among which curly birch has probably become differentiated. We argue that the introgressive hybridization of species observed now and then in the birch genus may be of the main reasons for the problems with definite taxonomic identification of silver birch and downy birch. It is also remarked that curly birch, although meeting the conventional biological criteria of a species, is still regarded a variety of silver birch. Having analyzed the population-genetic features of members of the genus Betula L., the authors conclude that the species status of silver birch and downy birch should be retained in spite of the identification difficulties and that instating curly birch as a separate biological species is advisable. We emphasize the importance and relevance of studying the population-genetic features of both common and rare members of the Betula genus to enable the development of efficient methods and practices of their selective breeding and reproduction of the most valuable genotypes as a solid scientific foundation for sustainable forest management.

Genetic characterization of non-O1/non-O139 <i>Vibrio cholerae</i> mobilome: a strategy for understanding and discriminating emerging environmental bacterial strains

Acute diarrhea and cholera (AWD/C) result in more than 21000 to 143000 global mortality annually and are associated with Vibrio cholerae. The pathogen has shown increasing evolutionary/emerging dynamics linked with mobilome or ubiquitous nature of mobile integrative genetic and conjugative elements (MIGCE), however, such dynamics are rarely reported amongst somatic-antigen non-agglutinating Type-1/-139 V. cholerae (SA-NAG-T-1/139Vc). The study reports the genetic detection of mobilome-associated indices in SA-NAG-T-1/139Vc as a potential strategy for differentiating/discriminating emerging environmental bacteria. Presumptive V. cholerae isolates were retrieved from five water sources, while strains were characterized/serogrouped and confirmed using simplex and comparative-genomic-multiplex Polymerase Chain Reaction (PCR). Genomic island (GI-12det, GI-14det, GI-15det); Phages (TLC-phagedet, Kappa-phagedet) and ICEs of the SXT/R391 family genes (SXT/R391-ICEs integrase, SXT-Hotspot-IV, ICEVchInd5Hotspot-IV, ICEVchMoz10Hotspot-IV) were detected. Other rare ICE members such as the ICEVcBan8att gene and Vibrio Seventh Pandemic island detection (VSP-II Integrase, Prototypical VSP-II) were also detected. Results revealed that the 8.22% (61/742) SA-NAG-T-1/139Vc serogroup observed harbors the Vibrio Seventh Pandemic island integrase (34/61; 55.7%) and other rare genetic traits including; attB/attP (29/61; 47.5%, 14/61; 23%), integrative genetic elements (4/61; 6.56%), phage types (TLC-phagedet: 2/61; 3.28% and Kappa-phagedet: 7/61; 11.48%) as well as the integrase genes (INT1, Sul1, Sul2) (29/61: 47.5%; 21/61: 34.4%; 25/61: 41%). Such genetic detection of mobilome determinants/MIGCE suggests potential discriminatory tendencies amongst SA-NAG-T-1/139Vcwhich may be applied in mobilome typing of evolving/emerging environmental bacteria. The need to encourage the application of such mobilome typing indices and continuous study of these strains is suggestive of interest in controlling future potential emerging environmental strains.

Floral Nectar Production of Jaltomata grandiflora, a Rare Mexican Nightshade

Understanding morphological, phenological, or chemical characters that promote reproduction, or limit it, is particularly important for rare plants. Jaltomata grandiflora is a rare member of the nightshade family (Solanaceae) from Mexico. In floral nectar, the mean cumulative sugar content per flower was 0.9 mg during the pistillate phase (day 1) and was significantly higher (1.25 mg) during the hermaphroditic phase (day 2). The mean cumulative nectar volume per flower was 0.99 µL during the pistillate phase and was higher (1.36 µL) but not significantly higher during the hermaphroditic phase. The mean sugar concentration (oBrix) was 67.8 during the pistillate phase and slightly higher (70.3) but not significantly higher during the hermaphroditic phase.

Loveringite from the Khamal Layered Mafic Intrusion: The First Occurrence in the Arabian Shield, Northwest Saudi Arabia

Loveringite, a rare member of the crichtonite group with nominal formula (Ca,Ce)(Ti,Fe,Cr,Mg)21O38, was found in the Khamal layered mafic intrusion, the first known locality for this mineral in the Arabian Shield. The Khamal intrusion, a large post-collisional mafic complex, is lithologically zoned, bottom to top, from olivine gabbro through gabbronorite, hornblende gabbro, anorthosite, and diorite to quartz diorite. Loveringite is found near the base of the complex, as an intercumulus phase in olivine gabbro. Most loveringite grains are homogeneous, although a few grains are zoned from cores rich in TiO2, Al2O3, Cr2O3, and CaO towards rims rich in FeO*, ZrO2, V2O3, Y2O3, and rare earth elements (REE). Petrographic relations indicate that loveringite formed after crystallization of cumulus olivine, pyroxenes, and plagioclase. Anhedral and corroded crystals of loveringite are surrounded by reaction rims of Mn-bearing ilmenite and baddeleyite, suggesting that the residual liquid evolved into and subsequently out of the stability field of loveringite. The budget of incompatible elements (Zr, Hf, REE, U, and Th) hosted in loveringite is anomalous for a primitive mafic liquid. Saturation in loveringite is likely the result of early contamination of the primary melt by anatexis of country rock, followed by isolation of evolving liquid in intercumulus space that restricted communication with the overlying magma chamber. The zoned crystals likely reflect diffusive equilibration between residual loveringite grains and their reaction rims of ilmenite.

Spatio-temporal patterns of Synechococcus oligotypes in Moroccan lagoonal environments

Synechococcus are unicellular cyanobacteria susceptible to environmental fluctuations and can be used as bioindicators of eutrophication in marine ecosystems. We examined their distribution in two Moroccan lagoons, Marchica on the Mediterranean coast and Oualidia on the Atlantic, in the summers of 2014 and 2015 using 16S rRNA amplicon oligotyping. Synechococcus representatives recruited a higher number of reads from the 16S rRNA in Marchica in comparison to Oualidia. We identified 31 Synechococcus oligotypes that clustered into 10 clades with different distribution patterns. The Synechococcus community was mainly represented by oligotype 1 (clade III) in Marchica. Cooccurring clades IV and I had an important relative abundance in Marchica in the summer of 2014, which is unusual, as these clades are widespread in cold waters. Moreover, Clades VII and subcluster “5.3” formed a sizeable percentage of the Synechococcus community in Marchica. Notably, we found low Synechococcus sequence counts in the Atlantic Lagoon. These results showed that the relative abundance of Synechococcus reads is not constant over space and time and that rare members of the Synechococcus community did not follow a consistent pattern. Further studies are required to decipher Synechococcus dynamics and the impact of environmental parameters on their spatial and temporal distributions.

Targeted Enrichment of Low-Abundance and Uncharacterized Taxon Members in Complex Microbial Community with Primer-Free FISH ProbesDesigned from Next Generation Sequencing Dataset.

Methods to obtain high-quality assembled genomic information of rare and unclassified member species in complex microbial communities remain a high priority in microbial ecology. Additionally, the supplementation of three-dimensional spatial information that highlights the morphology and spatial interaction would provide additional insights to its ecological role in the community. Fluorescent in-situ hybridization (FISH) coupling with fluorescence-activated cell sorting (FACS) is a powerful tool that enables the detection, visualization, and separation of low-abundance microbial members in samples containing complex microbial compositions. Here, we have described the workflow from designing the appropriate FISH probes from metagenomics or metatranscriptomics datasets to the preparation and treatment of samples to be used in FISH-FACS procedures.