127.7 Threatened and Endangered Species

127.7.1 Introduction

127.7.1.1 Overview

Threatened and endangered (T&E) species considerations for MoDOT and FHWA federally funded projects include potential impacts to rare plants, animals, critical habitat, and natural communities (e.g., caves, prairies, karst).

Federal laws require FHWA and MoDOT to thoroughly address any potential impacts their projects might have on federally listed T&E species and eliminate or minimize those impacts.

The state of Missouri also tracks the status of over 1,000 plant and animal species that are considered rare in the state. Of these, 64 are listed as state endangered (current as of the 2016 Missouri Species of Conservation Concern publication). The state Endangered Species Law and the Missouri Wildlife Code protect state listed species. MoDOT and FHWA projects in Missouri must also address potential impacts to state listed species.

127.7.1.2 Laws and Regulations

Additional Info

FHWA Feb 2015 non-fed designation letter

• Section 7 of the Endangered Species Act (ESA) of 1973 requires all federal agencies to carry out programs for the conservation of threatened and endangered species. It also requires agencies to conduct consultation with the U.S. Fish and Wildlife Service (FWS) regarding their projects and any measures that can be implemented to minimize or eliminate project impacts to federally listed species or designated critical habitat. In Missouri, FHWA has designated MoDOT as the only non-federal agency that can conduct ESA Section 7 consultation on their behalf. MoDOT must document effect determinations for all federally protected species that could occur in the project area and, if necessary, consult directly with FWS. Click for more information on the Endangered Species Act.

• The National Environmental Policy Act (NEPA) of 1969 (as amended) requires consideration of the physical environment for any project that uses federal funding or requires federal permits.

• The Missouri Cave Resources Act, Chapter 578, RSMo, protects caves from trespass, vandalism, contamination, and destruction.

• The Missouri Endangered Species Law, Chapter 252, RSMo, and 3 CSR 10 extends special protection to species that are listed as endangered in the state.

127.7.2 Process

The ESA requires federal agencies to evaluate every project and determine whether it could have a negative impact on any federally listed T&E species or their critical habitat. FHWA and MoDOT must use the best available scientific information to evaluate their projects and they must provide data to support their determination of impact. Under the ESA, no action can be taken that will jeopardize the continued existence of any federally listed threatened or endangered species or result in the destruction or adverse modification of critical habitat for such species. If an action will impact a T&E species or critical habitat, FHWA and MoDOT must consult with the FWS to determine how to eliminate or minimize those impacts. The assessment of potential impacts to T&E species should occur frequently throughout the development of each project because information regarding T&E species is constantly changing and being updated. To get an idea of how MoDOT assesses impacts to some species, refer to the MoDOT T&E Program Guidance video developed for the Local Public Agency program sponsors and consultants.

The district must complete and submit a Request for Environmental Services ( RES) to make the Design Division’s environmental section aware of a proposed project. Upon receiving an RES from the district, environmental staff will use publications, reports, and databases to screen the project and determine whether there are any known locations of federally or state listed species, critical habitat, or rare natural communities within the project limits or whether the project has the potential to impact a species that occurs nearby. The environmental specialist may also coordinate with FWS and the Missouri Department of Conservation (MDC) to determine whether the project is likely to impact any sensitive biological resources.

Missouri is home to 14 species of bats. Three of these species are federally protected and call Missouri caves and forests home. Occasionally, they also call our infrastructure “home”, at least temporarily. Bats can form colonies on or in bridges or use them as temporary day or night roosts, sleeping during the day, or stopping over at bridges to rest at night while feeding. Only one of these photos shows bats in a “natural” habitat; the top left photo is of Indiana bats clustering in a cave, which would be during winter hibernation. The rest are all photos of bats, even federally protected species, taking advantage of the cracks and crevices in our bridge structures. MoDOT environmental takes care to check our bridges for signs of bat use prior to bridge rehabilitation or replacement projects. If you do ever see bats utilizing bridges, please do not disturb them and report the occurrence to the Environmental Staff at MoDOT.

Video

Tumbling Creek Outflight

This video is an example of nightly summer activity at a gray bat colony in southwest Missouri as the maternity colony prepares to exit the cave for nighttime feeding. Tens of thousands of bats call this cave home every summer. MoDOT Environmental Section organizes a Highways, Caves, and Karst workshop once or twice a year for employees to travel to this cave and learn about karst, surface-to-groundwater connections and cave ecosystems.

If the project screening and coordination with the resource agencies do not document the presence of any federally listed species or critical habitat, then the ESA requires no further coordination at that time. In a response to the RES, the environmental specialist will indicate that the project is clear of any T&E species constraints for that phase of the project’s development. However, the project will need to be reevaluated at each stage of development.

127.7.2.1 District Responsibilities

The district is responsible for submitting an RES at each project milestone or annually if it has been a year since the last RES was submitted. Timely submittal of an RES is particularly important for T&E species because information on this topic can change rapidly. The district may be asked to provide additional detailed information about the project if necessary. The district may need to work with environmental staff and the U.S. Fish and Wildlife Service to determine measures that could be implemented to minimize the project’s impacts on T&E species. It is important that the district be involved in this process to assure that any suggested changes to the project are feasible for MoDOT.

127.7.2.2 Environmental Section Responsibilities

Upon receiving a completed RES from the district, environmental staff will review the project details, make impact evaluations, and provide the district with information about any potential environmental issues. Environmental staff will also specify what actions need to occur next in order to resolve these environmental issues and who needs to perform those actions (the district or the environmental section). Environmental staff, with help from district staff on technical information related to transportation project techniques, will handle all coordination with the resource agencies (i.e., U.S. Fish and Wildlife Service, Missouri Department of Conservation, etc.) and obtain any necessary clearances from these agencies. Environmental staff will also conduct any necessary surveys for T&E species that can be handled with MoDOT resources or they will coordinate any surveys that cannot be handled with MoDOT resources. The Environmental Section will maintain all written effect determinations for listed species being considered for each project.

If it is determined that a federally listed T&E species, critical habitat, or other sensitive biological resource is present or is likely to occur within the project limits, FHWA and MoDOT are required to complete ESA consultation with the FWS. The ESA describes two types of consultation, informal and formal. Informal consultation is required when a project May Affect, but is Not Likely to Adversely Affect a listed species. Formal consultation is required when a project is Likely to Adverse Affect a listed species of its critical habitat. Should formal consultation become necessary, FHWA and MoDOT would work through the process together.

Informal Consultation

Informal consultation is conducted when a T&E species or critical habitat is known, or likely to occur, in the area of a proposed project but MoDOT (acting for FHWA) has determined that the project is “not likely to adversely affect” the species. Informal consultation can only be done if FHWA and MoDOT can provide data to show that they have removed all potential for their project to have an adverse effect on the species or its critical habitat. Informal consultation usually involves MoDOT environmental staff submitting a letter to FWS describing the project and providing information to show that the project is not likely to adversely affect the species. However, before the letter can be written, the environmental specialist may need to conduct site visits, coordinate with personnel from FWS and MDC, or facilitate hiring consultants to conduct research to obtain additional information about the species or the habitat. The environmental specialist will also coordinate with the district to obtain specific details about the project and to determine what project modifications would be feasible (e.g., no tree cutting during bat breeding season). Once the letter is submitted to the FWS, they usually respond within 30 days. If they concur with the “not likely to adversely affect” determination, then additional clarification and protection measures may be needed. If adverse effect still cannot be removed, then formal consultation would likely be necessary. Informal consultation starts with discussions of the project details with FWS and should begin early in project development. Informal consultation should be submitted three to six months prior to letting to allow time to complete the process and avoid project delays.

Range-wide Programmatic Informal Consultation for Indiana Bat and Northern Long-eared Bat

A project may qualify for consultation under a programmatic agreement for summer bat habitat impacts if certain conditions can be met. USFWS and FHWA entered into an agreement in April 2015 for streamlining consultation for projects that are “not likely to adversely affect” Indiana and northern long-eared bats. More information about this programmatic consultation agreement is available. Generally, if the suitable bat summer habitat trees to be removed for the project are entirely within 100 ft. of the existing road, and MoDOT and FHWA agree to seasonal tree clearing (i.e. clearing suitable bat habitat only between November 1 and March 31) then the project likely qualifies for programmatic consultation. This involves MODOT environmental staff submitting a form to FWS describing project details and verifying the project meets the programmatic consultation criteria. The justification for this submittal is taken from the evaluation of the project impacts. It will be necessary to commit to seasonal tree clearing restrictions. Once the form is submitted to the FWS, they have 14 days to ask for additional information. If there is no comment during that time, the project has automatic concurrence for Indiana and northern long-eared bat impacts. If “no effect” determinations are made for all other species, then Section 7 ESA consultation is complete and MoDOT will notify the district with environmental clearance.

Formal Consultation

Formal consultation is required when it is determined that a project is likely to adversely affect a federally listed species or critical habitat. The purpose of formal consultation is to identify and resolve potential conflicts between a proposed project and a T&E species or critical habitat. The process is initiated when FHWA submits a letter to the FWS requesting formal consultation for a project; a biological assessment (BA) usually accompanies the letter. MoDOT environmental staff (acting for FHWA) prepare the BA, which contains specific, detailed information on a federally listed threatened or endangered species or designated critical habitat that may be present in or near the project area. The BA also includes an impact assessment and describes conservation measures that will be implemented to eliminate or minimize the project’s impacts on the species. As with informal consultation, research may be necessary to collect additional information on the species. Because of all the information that needs to go into a BA and the importance of having the most current information available, preparing a BA takes a considerable amount of time. BA preparation requires close coordination with the district to determine specific information about the project and what modifications might be feasible. The ESA gives the FWS 135 days to respond once FHWA initiates formal consultation and submits the information necessary for the FWS to evaluate the project and its potential impacts. The FWS response includes a Biological Opinion in which the FWS provides reasonable and prudent measures that need to be incorporated into the project. These reasonable and prudent measures are intended to eliminate or minimize any negative impacts to the species. The Biological Opinion may also include an incidental take statement that allows the take of a specified number of individuals of that species. When possible, formal consultation should begin at least one to two years prior to letting to allow time to complete the process.

127.7.3 Project Development Milestones

127.7.3.1 Initial Screening Stage

At the initial project screening stage, the environmental specialist performs a cursory identification of potential issues related to T&E species or other sensitive biological resources. The environmental specialist reviews recent publications, reports, and databases related to these resources to determine whether any T&E species are known to occur in the area and the likelihood that the project will have a negative impact on such species or other biological resources.

The district initiates this process by submitting an RES to the Design Division. A complete RES should include the amount of tree clearing, if any, whether or not bridges in the project area are exempted out of the project, if there is evidence of birds or bats using the underside of bridges or box culverts as habitat, a map of the project locations, complete footprint and aerial of the project limits, and a full description of the project components. If the RES is completed in its entirety, usually no additional information will be required from the district. Any findings pertinent to the project will be relayed to the district in the RES response, which will also indicate what type of coordination with FWS is believed necessary, if any.

127.7.3.2 Location/Conceptual Plan Stage

At the location/conceptual plan stage, the environmental specialist screens the project again but may also contact resource and regulatory agencies to determine whether they have any concerns with the project.

The district initiates this process by submitting an RES to the Design Division or for projects that require an Environmental Assessment ( EA) or an Environmental Impact Statement ( EIS), the Design Division and the district will determine when to begin this process. The district may be required to obtain and submit additional information about the project at this stage. Any findings pertinent to the project will be relayed to the district in the RES response and through core team participation.

127.7.3.3 Interagency Coordination (Scoping)

If the project requires an Environmental Assessment (EA) or an Environmental Impact Statement (EIS), environmental staff will contact the resource and regulatory agencies to solicit their comments concerning potential impacts to T&E species or other sensitive biological resources. Consultant documents will include the written correspondence to and from the resource agencies during the scoping portion of any project.

127.7.3.4 Development of Alternatives

Interagency coordination must be initiated prior to the development of alternatives and is to be used to guide alternatives development. This activity fulfills the requirements of NEPA and FWCA as they relate to the selection of alternatives and the information obtained is used in the EA or EIS documentation.

127.7.3.5 Preliminary Plans Stage

At the preliminary plans stage, if no T&E issues have been identified to date, a process similar to that described for the initial project screening is repeated. The district initiates this process by submitting an RES to the Design Division. The environmental specialist screens the project and verifies that no new information has become available since the last screening. Any new findings pertinent to the project will be relayed to the district in the RES response and the environmental specialist will discuss appropriate actions with the project manager.

At this stage if it has been determined that the project could have an impact on a T&E species or critical habitat, the environmental specialist will begin coordinating with FWS to determine the type of consultation (formal or informal, as discussed in EPG 127.7.2 Process) that will be necessary. Depending on the project’s schedule, the extent of the potential impact, the type of consultation necessary, the species impacted, etc., the environmental specialist may begin consultation with FWS at this stage. Many MoDOT projects require U.S. Army Corps of Engineers Section 404 permits and some require U.S. Coast Guard permits. These agencies will not issue permits until all ESA requirements have been completed with the FWS so it is important that coordination with the FWS begin early in the project development process. The district will need to provide additional information during consultation with FWS.

127.7.3.6 Right of Way Plan Stage

At the right-of-way plan stage, if no T&E issues have been identified to date, the process described for earlier stages is repeated. The district initiates this process by submitting an RES to the Design Division, whereupon the environmental specialist will screen the project and make sure no new information has become available since the last screening. Any new findings pertinent to the project will be relayed to the district in the RES response and the environmental specialist will discuss appropriate actions with the project manager.

At this stage, if it has been determined that the project could have an impact on a T&E species or critical habitat, consultation with FWS should be underway or should begin (refer to previous discussion in EPG 127.7.2 Process for details on consultation). The district will be asked to provide additional information about the project during consultation. District staff may also be asked to attend meetings/site visits and to help develop or comment on suggested conservation measures. The environmental specialist will keep the district involved throughout the consultation process to assure that no commitments are made that cannot be met.

127.7.3.7 Final Design Stage

At final design stage, if no T&E issues have been identified to date, the process described for earlier stages is repeated. The district submits an RES to the Design Division and the environmental specialist screens the project to verify that no new information has become available. Any new findings pertinent to the project are relayed to the district in the RES response and the environmental specialist will discuss appropriate actions with the project manager. If no threatened or endangered species issues are identified, the district will be notified that T&E issues are clear for this project.

At this stage, if it has been determined that the project could impact a T&E species or critical habitat, consultation with the FWS should be underway or already completed. The environmental specialist will keep the district informed of the status of this consultation and the projected completion date.

Job special provisions (JSPs) may be required to assure that the project avoids or minimizes impacts to known populations of T&E species, their habitats, or other sensitive biological resources. These JSPs are developed through coordination with the district, the environmental section, and the resource agencies, but the district usually writes the JSPs.

When special conservation measures are necessary to minimize or offset a project’s impacts, the district works with the environmental section to complete a plan that specifies how such measures will be accomplished and implemented. This plan must be approved by the appropriate regulatory agencies prior to letting. MoDOT should complete ESA consultation before the plans, specifications, and estimates (PS&E) submission date.

127.7.3.8 Letting

If any threatened or endangered species issues were identified during any of the previous phases of project development, MoDOT must obtain clearance from the FWS confirming that Section 7 ESA consultation requirements have been completed. This must be obtained prior to letting the project; it is a violation of the ESA to commit resources that cannot be reversed to a project prior to completing the Section 7 consultation requirements. If no threatened or endangered species issues have been identified, the district will be notified that T&E issues are clear for this project.

127.7.3.9 Post-Letting Activities

MoDOT Working to Preserve Endangered Salamanders

Ever heard of an Ozark hellbender? It's an endangered salamander that the Missouri departments of Transportation and Conservation, U.S. Fish and Wildlife Service, and the Army Corps of Engineers are working to protect. MoDOT learned of a population of this funny-looking creature near a bridge maintenance project. The project site is one of the few places in the state where the hellbender is found.

There are two species of hellbender in Missouri. The Eastern hellbender, the more common of the two species, is still rare in the state and is listed as state-endangered by the Missouri Department of Conservation. But the Ozark hellbender is even more uncommon—it is listed as endangered at both the state and federal levels. Both species are large salamanders that need fresh flowing uncontaminated water, a clean environment and a little bit of understanding. Hellbenders are among the largest salamanders in the world, but they are peaceful, non-venomous and they eat crayfish and the occasional minnow. Ozark hellbender populations are declining because of habitat loss from silt caused by poorly managed land use and development. Because the salamanders are endangered, MoDOT's Bridge Maintenance and Environmental staff had to work together, and with federal and state agencies, to develop plans to save an old bridge without harming the hellbenders.

"Most of the time, we work with designers to avoid impacting endangered species and their habitats," said Senior Environmental Specialist Chris Shulse. "In this case we were dealing with a situation where suitable habitat for the animals was within the eroded piers of the bridge itself. Since the project involved fixing the piers by filling them with concrete, we were not only taking away suitable habitat, we were potentially entombing any hellbenders living inside the piers. We had to carefully plan how it was going to be done.”

Working together, MoDOT, MDC, the Corps and the FWS decided to allow biologists to dive and search around the bridge, and within the eroded piers, for hellbenders prior to starting work. Any hellbenders discovered during the search would be removed and re-located to a safe area. Since hellbenders can wedge themselves into tight spaces where they could be hard to find, MoDOT’s bridge maintenance personnel made changes to their plans that allowed any unseen hellbenders to escape prior to pouring the concrete. They also made sure their design for forming up the concrete was as tight as possible to avoid contaminating the clean waters of the hellbenders’ environment.

MoDOT has a responsibility to protect endangered species and the environment while delivering transportation projects on time and within budget, although that balancing act can sometimes get tricky.

Great strides are being made to keep Ozark hellbender populations healthy in Missouri. When the project is finished, the bridge will remain open to traffic, and the habitat conditions around the bridge will continue to be suitable for hellbenders as well as for other aquatic life. MDC will continue to monitor the hellbenders in the stream to ensure these amphibians have a healthy chance of survival.

At this stage, the primary concern is assuring that all JSPs and special conservation measures are being implemented. Prior to letting, MoDOT resident engineers and inspectors should be informed of all issues and any special requirements or JSPs. Contractors should also be informed of these issues prior to construction. If MoDOT fails to implement the measures agreed upon during consultation with the FWS, the project can be shut down immediately and FHWA and MoDOT will have to start the consultation process over again. This can create lengthy project delays and result in significant fines.

127.7.4 Maintenance Activities

In certain areas, maintenance activities such as spraying, mowing, tree cutting, chip seals, etc. could impact a threatened or endangered species. These issues will be in specific areas and will be handled on a case-by-case basis. Roadside maintenance personnel have information regarding sensitive areas and they may assist the district in dealing with these issues. In other cases, the Design Division environmental specialist will notify the district of the issue and will coordinate with maintenance personnel and others in the district to determine the appropriate course of action (e.g., general maintenance guidance, signing area restricting activities such as mowing, spraying, excavating, etc.).

127.7.5 Bridge Demolition

Bridge demolition projects such as bridge blasting or the possibility of bridge material being knocked into the stream can have serious impacts to rare aquatic species. Demolition activities are to be described in each RES that is submitted for the construction of the new bridge, or a separate RES should be submitted well in advance of the letting date for the project. Either way, the process is the same as described previously for any other project. It is critical that the district make it clear that a bridge demolition will be part of the project or submit a separate RES for the demolition because there could be numerous T&E issues with a demolition that may not exist if the project simply involved construction of a new bridge.

127.7.6 Migratory Birds

127.7.6.1 Overview

MoDOT frequently encounters the nests of bird species protected by the Migratory Bird Treaty Act of 1918 (MBTA) while conducting bridge repairs and replacements. Several bird species protected by the Act commonly construct their nests on the underside of bridge decks and on the substructure. These most often include cliff swallows, barn swallows, Eastern phoebes, and American robins. Cliff swallows build their gourd-shaped mud nests in colonies, sometimes containing hundreds of nests. Often, these nests are found on bridges over water but they can also occur on bridges over major highways and railroads, particularly if the bridge is in a floodplain or near permanent water. Barn swallows also build mud nests, but they are cup-shaped and not enclosed like cliff swallows. They will also nest in colonies, but usually these are much smaller than those of cliff swallows. Eastern phoebe and American robin nests are frequently found on smaller bridges over small rivers. Usually they are on the top of substructure steel components and near the abutments. They are not colony nesters but sometimes 3 or 4 nests can be found on a single bridge. Other MBTA-protected species can also be found nesting on bridges, but they are not common.

State endangered Peregrine Falcon juvenile nesting area discovered while preparing to paint steel substructure on Jefferson Barracks Bridge in St. Louis area. (Photo credit: Tom Reed, St. Louis District, 5-23-12)

Several bird species that are not protected by the MBTA are often seen nesting on bridges. These include pigeons (rock doves), European starlings, and house sparrows. These species are all non-native introductions to the US and therefore, they are not protected by the MBTA.

127.7.6.2 Laws and Regulations

The Migratory Bird Treaty Act of 1918 makes it illegal for anyone to take, possess, import, export, transport, sell, purchase, barter, or offer for sale, purchase or barter any migratory bird, or the parts, nests or eggs of such a bird except under the terms of a valid permit issued pursuant to Federal regulations. The migratory bird species protected by the act are listed in 50 CFR 10.13. “Take” refers to killing adults, eggs or young of the bird species protected by the act.

127.7.6.3 Process

All projects that involve impacts to the underside of bridge decks, or the substructure, should be checked for the presence of nesting birds. This inspection can be performed by the district, bridge crews, or Environmental staff. Presence of nests should be noted on the RES. For LPA projects, the project sponsor or their consultant is expected to perform the inspection and report it on the Request for Environmental Review (RER).

Inspections should take place within a year of the anticipated letting date. If no nests are noted, the project will be cleared and nothing further is required. If nests are noted, a Job Special Provision will need to be placed in the contract that provides guidance on how to avoid violating the MBTA. Often, removal of the old, inactive nests (those without eggs or young) before the project starts, and maintenance of the bridge in a nest-free condition until construction, is necessary. Nest removal should be done in the non-breeding season. Generally speaking, the assumed active breeding season for the majority of the birds that would use bridge and culvert structures as habitat is between April 1 and July 31. However, these are just general dates and no active bird nests should be disturbed without a permit, even outside of these dates.

MoDOT has also worked with the United States Department of Agriculture (USDA) Animal and Plant Health Inspection Service (APHIS) and the US Fish and Wildlife Service (USFWS) to obtain depredation permits for removal of active nests containing eggs from bridges. These permits are only used as a last resort (avoidance measures must be used first) and no young or adults are allowed to be killed. The permits allow a project to continue without delay if a nest is missed while maintaining a nest-free condition.

127.7.6.4 District Responsibilities

This district is responsible for reporting any nests known to be present on the structure when submitting and RES. If nests are present, the JSP for avoidance will be used and must be followed. If the district would like to include any bridges on the annual depredation permit, they must notify their Environmental contact. Bridges can be added to the permit at any time, but it is best to include it in the initial permit application (usually submitted to APHIS and USFWS each January). Removal of active nests under the depredation permit requires annual reporting to the USFWS. The Environmental contact will distribute a form to district Design and Construction Management staff late in the calendar year for reporting nests taken during the previous construction season.

127.7.6.5 Environmental Section Responsibilities

During RES reviews, Environmental Specialists will review the project scope and determine if the project has the potential to result in take of MBTA-protected species. If so, the Environmental Specialist will work with the district to determine if nests are present on the structure (if not already known) including inspections conducted by Environmental staff. The Environmental Specialist will confirm with the district the JSP will be used, and whether or not a depredation permit will be needed, prior to clearing Migratory Birds on the RES. The Environmental Specialist will apply for depredation permits, if needed or requested, based on information provided by the district. If a project is already under construction, and nests are noted on the bridge, it will be the responsibility of the Environmental Specialist to determine if the nests are active, if they belong to an MBTA-protected species, and to provide the district with options to avoid violations of the MBTA.