Detecting bedform migration from high-resolution multibeam bathymetry in Portsmouth Harbor, New Hampshire, USA

A study was undertaken to quantify dune migration in Portsmouth Harbor, New Hampshire, USA from repeat high-resolution multibeam echosounder (MBES) surveys. Repeat MBES surveys were conducted in June 2007 and July 2008 over periods ranging from 6 hours to 7 days in order to capture the response of dune morphology to ebb-flood and spring-neap tidal cycles. A new technique was developed for detecting bedform migration. This approach utilizes a fingerprint-detection algorithm (Bishnu et al., 2002) to convert the bathymetric surface to a binary map of bedform crests, which are subsequently tracked using a spatial cross-correlation technique (Duffy and Hughes-Clarke, 2005). Acoustic current-meter observations from July 2008 provided context for the observed bedform-migration patterns, and were subsequently used to compute bed shear stress. Results indicate that dune migration occurred over periods as short as 6 hours. Dune migration distances in excess of 2 m were observed over 6- and 7-day periods

Detecting bedform migration in Portsmouth Harbor, New Hampshire, USA, on relatively short spatial and temporal scales

Multibeam echosounder (MBES) systems have enjoyed recent popularity as a tool in bedform-migration studies due to their ability to produce high-resolution seafloor imagery with complete bottom coverage. Although shallow-water MBES systems may achieve decimeter-scale data resolution, the use of MBES to successfully detect and quantify bedform migration on short time-scales (days to weeks) where the migration distance is relatively small (\u3c 1 m) remains limited by positioning uncertainty. In this study we evaluate short-term bedform migration and sediment transport in a bedform field at the entrance to Portsmouth Harbor, New Hampshire, USA. Bedform dynamics over 24-hour and multi-day periods were determined from high-resolution bathymetry (0.25 m grid resolution) acquired with a Kongsberg EM3002D MBES system. Position, heading and attitude data were acquired with an Applanix POS/MV system with integrated real-time kinematic GPS correctors, providing a horizontal positioning uncertainty of \u3c 0.1 m at the GPS receiver. MBES surveys were conducted on June 8, 14 and 15 in 2007 and July 3 and 9 in 2008. Acoustic current meters were deployed at two stations within the survey area in 2008 to provide simultaneous observations of current velocities at a height of 1 m above the bottom. A new approach was developed and used for detecting and quantifying bedform migration from the bathymetry. Our approach utilizes a ridge-extraction algorithm to derive a binary map of dune-crest positions from the bathymetric surface, and then calculates the displacements of small (6.25 m2) subsets of dune crest. Preliminary results indicate that bedform migrations of ≥ 0.1 m were successfully resolved. Morphology of the bedform field is dominated by medium and large, two-dimensional, asymmetrical subaqueous dunes (0.4 to 0.8 m height, 8 to 16 m wavelength). Small, two-dimensional, ebb-oriented subaqueous dunes (0.3 m height, 5 m wavelength) line the eastern margin of the bedform field, which is adjacent to the channel thalweg. Initial analysis indicates that bedforms are active on 24-hour and multi-day cycles, with migrations of \u3e 1.2 m observed on multi-day cycles. The highest bedform-migration rates are observed along the eastern margin where smaller dunes occur. In 2007 we observed a reciprocal pattern of bedform migration, in which dunes in the western half of the bedform field migrated in a net flood (northward) direction and dunes in the eastern half migrated in a net ebb (southward) direction. In 2008, the eastern dune population was still active and southward-migrating, though the western half of the bedform field appeared to be inactive. The observed pattern of bedform migration is supported by current-meter data from six tidal cycles (spring tidal conditions) during the 2008 experiment, which reveal a strong cross-channel difference in the flood and ebb currents. The data indicate ebb-current dominance in the eastern half of the study area and flood-current dominance in the western half of the study area. Individual bedforms cannot be tracked over the annual period (2007 to 2008) without a higher survey-repetition rate, suggesting that annual migration distances are comparable with or greater than the bedform wavelength, and/or that bedform morphology changes significantly over time-scales shorter than one yea

Family- and Genus-Level 16S rRNA-Targeted Oligonucleotide Probes for Ecological Studies of Methanotrophic Bacteria

Methanotrophic bacteria play a major role in the global carbon cycle, degrade xenobiotic pollutants, and have the potential for a variety of biotechnological applications. To facilitate ecological studies of these important organisms, we developed a suite of oligonucleotide probes for quantitative analysis of methanotroph-specific 16S rRNA from environmental samples. Two probes target methanotrophs in the family Methylocystaceae (type II methanotrophs) as a group. No oligonucleotide signatures that distinguish between the two genera in this family, Methylocystis and Methylosinus, were identified. Two other probes target, as a single group, a majority of the known methanotrophs belonging to the family Methylococcaceae (type I/X methanotrophs). The remaining probes target members of individual genera of the Methylococcaceae, including Methylobacter, Methylomonas, Methylomicrobium, Methylococcus, and Methylocaldum. One of the family-level probes also covers all methanotrophic endosymbionts of marine mollusks for which 16S rRNA sequences have been published. The two known species of the newly described genus Methylosarcina gen. nov. are covered by a probe that otherwise targets only members of the closely related genus Methylomicrobium. None of the probes covers strains of the newly proposed genera Methylocella and “Methylothermus,” which are polyphyletic with respect to the recognized methanotrophic families. Empirically determined midpoint dissociation temperatures were 49 to 57°C for all probes. In dot blot screening against RNA from positive- and negative-control strains, the probes were specific to their intended targets. The broad coverage and high degree of specificity of this new suite of probes will provide more detailed, quantitative information about the community structure of methanotrophs in environmental samples than was previously available