A metagenome for lacustrine Cladophora (Cladophorales) reveals remarkable diversity of eukaryotic epibionts and genes relevant to materials cycling

Periphyton dominated by the cellulose-rich filamentous green alga Cladophora forms conspicuous growths along rocky marine and freshwater shorelines worldwide, providing habitat for diverse epibionts. Bacterial epibionts have been inferred to display diverse functions of biogeochemical significance: N-fixation and other redox reactions, phosphorus accumulation, and organic degradation. Here, we report taxonomic diversity of eukaryotic and prokaryotic epibionts and diversity of genes associated with materials cycling in a Cladophora metagenome sampled from Lake Mendota, Dane Co., WI, USA, during the growing season of 2012. A total of 1,060 distinct 16S, 173 18S, and 351 28S rRNA operational taxonomic units, from which >220 genera or species of bacteria (~60), protists (~80), fungi (6), and microscopic metazoa (~80), were distinguished with the use of reference databases. We inferred the presence of several algal taxa generally associated with marine systems and detected Jaoa, a freshwater periphytic ulvophyte previously thought endemic to China. We identified six distinct nifH gene sequences marking nitrogen fixation, >25 bacterial and eukaryotic cellulases relevant to sedimentary C-cycling and technological applications, and genes encoding enzymes in aerobic and anaerobic pathways for vitamin B12 biosynthesis. These results emphasize the importance of Cladophora in providing habitat for microscopic metazoa, fungi, protists, and bacteria that are often inconspicuous, yet play important roles in ecosystem biogeochemistry

Comparative ultrastructure of plasmodesmata of Chara and selected bryophytes: towards an elucidation of the evolutionary origin of plant plasmodesmata

We have used transmission electron microscopy to examine plasmodesmata of the charophycean green alga Chara zeylanica, and of the putatively early divergent bryophytes Monoclea gottschei (liverwort), Notothylas orbicularis (hornwort), and Sphagnum fimbriatum (moss), in an attempt to learn when seed plant plasmodesmata may have originated. The three bryophytes examined have desmotubules. In addition, Monoclea was found to have branched plasmodesmata, and plasmodesmata of Sphagnum displayed densely staining regions around the neck region, as well as ring-like wall specializations. In Chara, longitudinal sections revealed endoplasmic reticulum (ER) that sometimes appeared to be associated with plasmodesmata, but this was rare, despite abundant ER at the cell periphery. Across all three fixation methods, cross-sectional views showed an internal central structure, which in some cases appeared to be connected to the plasma membrane via spoke-like structures. Plasmodesmata were present even in the incompletely formed reticulum of forming cell plates, from which we conclude that primary plasmodesmata are formed at cytokinesis in Chara zeylanica. Based on these results it appears that plasmodesmata of Chara may be less specialized than those of seed plants, and that complex plasmodesmata probably evolved in the ancestor of land plants before extant lineages of bryophytes diverged

Episodic Disturbance from Boat Anchoring Is a Major Contributor to, but Does Not Alter the Trajectory of, Long-Term Coral Reef Decline

Isolating the relative effects of episodic disturbances and chronic stressors on long-term community change is challenging. We assessed the impact of an episodic disturbance associated with human visitation (boat anchoring) relative to other drivers of long-term change on coral reefs. A one-time anchoring event at Crab Cove, British Virgin Islands, in 2004 caused rapid losses of coral and reef structural complexity that were equal to the cumulative decline over 23 years observed at an adjacent site. The abundance of small site-attached reef fishes dropped by approximately one quarter after the anchoring event, but this drop was not immediate and only fully apparent two years after the anchoring event. There was no obvious recovery from the impact, and no evidence that this episodic impact accelerated or retarded subsequent declines from other causes. This apparent lack of synergism between the effect of this episodic human impact and other chronic stressors is consistent with the few other long-term studies of episodic impacts, and suggests that action to mitigate anchor damage should yield predictable benefits

The genus Cladophora Kutzing (Ulvophyceae) as a globally distributed ecological engineer

The green algal genus Cladophora forms conspicuous nearshore populations in marine and freshwaters worldwide, commonly dominating peri-phyton communities. As the result of human activities, including the nutrient pollution of nearshore waters, Cladophora-dominated periphyton can form nuisance blooms. On the other hand, Cladophora has ecological functions that are beneficial, but less well appreciated. For example, Cladophora has previously been characterized as an ecological engineer because its complex structure fosters functional and taxonomic diversity of benthic microfauna. Here, we review classic and recent literature concerning taxonomy, cell biology, morphology, reproductive biology, and ecology of the genus Cladophora, to examine how this alga functions to modify habitats and influence littoral biogeochemistry. We review the evidence that Cladophora supports large, diverse populations of microalgal and bacterial epiphytes that influence the cycling of carbon and other key elements, and that the high production of cellulose and hydrocarbons by Cladophora-dominated periphyton has the potential for diverse technological applications, including wastewater remediation coupled to renewable biofuel production. We postulate that well-known aspects of Cladophora morphology, hydrodynamically stable and perennial holdfasts, distinctively branched architecture, unusually large cell and sporangial size and robust cell wall construction, are major factors contributing to the multiple roles of this organism as an ecological engineer

Comparing monitoring data collected by volunteers and professionals shows that citizen scientists can detect long-term change on coral reefs

Citizen science is increasing and can complement the work of professional scientists, but the value of citizen data is often untested. We therefore compared the long-term changes to coral reefs that were detected by a professional and volunteer monitoring program, operated by University of Rhode Island (URI) staff and Reef Check volunteers, respectively. Both groups monitored reefs in the British Virgin Islands from 1997 to 2012 but mostly monitored different sites (URI 8 sites and Reef Check 4 sites). When URI staff visited the Reef Check sites to perform a side-by-side to comparison, Reef Check fish density estimates were consistently higher than those made by URI observers but benthic indicators showed better agreement. When long-term trends were compared, the two programs detected qualitatively similar trends in the % cover of live coral and coral rubble, but temporal changes in the cover of other benthic indicators were less consistent. The URI program detected a widespread increase in parrotfish densities and a decline in snappers, whereas the Reef Check surveys detected no consistent changes in any fish density indicators. Overall, site-specific temporal trends revealed by the URI program were more often statistically significant than those from Reef Check (twice as often for benthic taxa, and five times as often for fish taxa), which implies greater precision of the scientists’ counts. Nonetheless, volunteers were able to detect important changes in benthic communities and so have a valuable role to play in assessing change on coral reefs

Peat Moss–Like Vegetative Remains from Ordovician Carbonates

Premise of research. Climatically favorable conditions correspond with fossil evidence for dramatic Ordovician marine biodiversification, but coeval terrestrial biodiversity is less well understood. Although diverse Middle and Late Ordovician microfossils are interpreted as reproductive remains of early bryophyte-like land plants (consistent with molecular data indicating pre-Ordovician embryophyte origin), the vegetative structure of Ordovician plants remains mysterious, as do relationships to modern groups. Because distinctive fungal microfossils indicating land plant presence were previously reported from Ordovician carbonate deposits in Wisconsin, we examined another nearby outcrop for additional evidence of terrestrial biodiversification. Methodology. Replicate collections were made from well-understood 455–454 Ma Platteville Formation carbonates of relatively low porosity and hydraulic conductivity. We employed measures to avoid contamination, and organic remains extracted by acid maceration were characterized by light and scanning electron microscopy and energy-dispersive X-ray spectroscopy. Pivotal results. Multicellular organic fragments displayed distinctive cellular features shared with modern vegetative peat mosses but differed from modern materials, e.g., fossil presence of mineral coatings, absence of epibionts. Biometric features of mosslike microfossils isolated from carbonates collected and macerated 12 yr apart by separate investigators did not differ. Putative peat moss remains occurred with foraminifera similar in frequency and thermal maturity to types previously described from the same formation. No diatoms, pollen, or other indicators of post-Ordovician environments were observed. Conclusions. The peat moss–like fragments described here are the oldest-known vegetative remains of land plants and the oldest fossils having distinctive features linking them to a modern plant group. These findings are consistent with peat moss recalcitrance properties that foster fossilization and molecular evidence that the peat moss lineage is 460–607 Ma of age. The new findings suggest that moss-dominated peatlands—recognized for globally significant roles in modern terrestrial biodiversity and C and N cycling—were present hundreds of millions of years earlier than previously thought

Building a Model of Collaboration Between Historically Black and Historically White Universities

Despite increases over the last two decades in the number of degrees awarded to students from underrepresented groups in science, technology, engineering, and mathematics (STEM) disciplines, enhancing diversity in these disciplines remains a challenge. This article describes a strategic approach to this challenge—the development of a collaborative partnership between two universities: the historically Black Elizabeth City State University and the historically White University of New Hampshire. The partnership, a type of learning organization built on three mutually agreed upon principles, strives to enhance opportunities for underrepresented students to pursue careers in the STEM disciplines. This article further describes six promising practices that framed the partnership, which resulted in the submission of nine proposals to federal agencies and the funding of four grants that led to the implementation, research, learning, and evaluation that followed

Micro-Net: A unified model for segmentation of various objects in microscopy images

Object segmentation and structure localization are important steps in automated image analysis pipelines for microscopy images. We present a convolution neural network (CNN) based deep learning architecture for segmentation of objects in microscopy images. The proposed network can be used to segment cells, nuclei and glands in fluorescence microscopy and histology images after slight tuning of input parameters. The network trains at multiple resolutions of the input image, connects the intermediate layers for better localization and context and generates the output using multi-resolution deconvolution filters. The extra convolutional layers which bypass the max-pooling operation allow the network to train for variable input intensities and object size and make it robust to noisy data. We compare our results on publicly available data sets and show that the proposed network outperforms recent deep learning algorithms

Fingerprinting the Cretaceous-Paleogene boundary impact with Zn isotopes

Numerous geochemical anomalies exist at the K-Pg boundary that indicate the addition of extraterrestrial materials; however, none fingerprint volatilization, a key process that occurs during large bolide impacts. Stable Zn isotopes are an exceptional indicator of volatility-related processes, where partial vaporization of Zn leaves the residuum enriched in its heavy isotopes. Here, we present Zn isotope data for sedimentary rock layers of the K-Pg boundary, which display heavier Zn isotope compositions and lower Zn concentrations relative to surrounding sedimentary rocks, the carbonate platform at the impact site, and most carbonaceous chondrites. Neither volcanic events nor secondary alteration during weathering and diagenesis can explain the Zn concentration and isotope signatures present. The systematically higher Zn isotope values within the boundary layer sediments provide an isotopic fingerprint of partially evaporated material within the K-Pg boundary layer, thus earmarking Zn volatilization during impact and subsequent ejecta transport associated with an impact at the K-Pg